Date: 2019-12-26 18:30:36 CET, cola version: 1.3.2
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First the variable is renamed to res_list.
res_list = rl
All available functions which can be applied to this res_list object:
res_list
#> A 'ConsensusPartitionList' object with 24 methods.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows are extracted by 'SD, CV, MAD, ATC' methods.
#> Subgroups are detected by 'hclust, kmeans, skmeans, pam, mclust, NMF' method.
#> Number of partitions are tried for k = 2, 3, 4, 5, 6.
#> Performed in total 30000 partitions by row resampling.
#>
#> Following methods can be applied to this 'ConsensusPartitionList' object:
#> [1] "cola_report" "collect_classes" "collect_plots" "collect_stats"
#> [5] "colnames" "functional_enrichment" "get_anno_col" "get_anno"
#> [9] "get_classes" "get_matrix" "get_membership" "get_stats"
#> [13] "is_best_k" "is_stable_k" "ncol" "nrow"
#> [17] "rownames" "show" "suggest_best_k" "test_to_known_factors"
#> [21] "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single method by, e.g. object["SD", "hclust"] or object["SD:hclust"]
#> or a subset of methods by object[c("SD", "CV")], c("hclust", "kmeans")]
The call of run_all_consensus_partition_methods() was:
#> run_all_consensus_partition_methods(data = m, mc.cores = 4, anno = data.frame(subtype = subtype),
#> anno_col = list(subtype = subtype_col))
Dimension of the input matrix:
mat = get_matrix(res_list)
dim(mat)
#> [1] 11268 173
The density distribution for each sample is visualized as in one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, top_annotation = HeatmapAnnotation(df = get_anno(res_list),
col = get_anno_col(res_list)), ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 4)
Folowing table shows the best k (number of partitions) for each combination
of top-value methods and partition methods. Clicking on the method name in
the table goes to the section for a single combination of methods.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_list)
| The best k | 1-PAC | Mean silhouette | Concordance | Optional k | ||
|---|---|---|---|---|---|---|
| SD:skmeans | 4 | 0.968 | 0.932 | 0.971 | ** | 2,3 |
| MAD:kmeans | 4 | 0.967 | 0.942 | 0.972 | ** | |
| ATC:NMF | 2 | 0.964 | 0.951 | 0.980 | ** | |
| MAD:skmeans | 4 | 0.959 | 0.927 | 0.969 | ** | 2,3 |
| SD:NMF | 4 | 0.945 | 0.928 | 0.969 | * | |
| ATC:skmeans | 4 | 0.942 | 0.904 | 0.951 | * | 2,3 |
| MAD:pam | 2 | 0.928 | 0.940 | 0.974 | * | |
| MAD:NMF | 4 | 0.921 | 0.913 | 0.962 | * | |
| CV:skmeans | 2 | 0.917 | 0.925 | 0.970 | * | |
| SD:mclust | 2 | 0.917 | 0.937 | 0.974 | * | |
| SD:kmeans | 4 | 0.907 | 0.917 | 0.963 | * | |
| ATC:kmeans | 2 | 0.905 | 0.924 | 0.970 | * | |
| MAD:mclust | 2 | 0.872 | 0.917 | 0.966 | ||
| CV:NMF | 2 | 0.815 | 0.883 | 0.953 | ||
| ATC:pam | 3 | 0.788 | 0.836 | 0.933 | ||
| SD:pam | 3 | 0.760 | 0.859 | 0.938 | ||
| CV:pam | 4 | 0.725 | 0.824 | 0.900 | ||
| CV:kmeans | 2 | 0.722 | 0.883 | 0.944 | ||
| ATC:mclust | 3 | 0.445 | 0.623 | 0.810 | ||
| CV:mclust | 4 | 0.423 | 0.632 | 0.800 | ||
| ATC:hclust | 3 | 0.329 | 0.500 | 0.708 | ||
| MAD:hclust | 2 | 0.280 | 0.649 | 0.825 | ||
| SD:hclust | 2 | 0.222 | 0.537 | 0.786 | ||
| CV:hclust | 2 | 0.135 | 0.609 | 0.755 |
**: 1-PAC > 0.95, *: 1-PAC > 0.9
Cumulative distribution function curves of consensus matrix for all methods.
collect_plots(res_list, fun = plot_ecdf)
Consensus heatmaps for all methods. (What is a consensus heatmap?)
collect_plots(res_list, k = 2, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 3, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 4, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 5, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 6, fun = consensus_heatmap, mc.cores = 4)
Membership heatmaps for all methods. (What is a membership heatmap?)
collect_plots(res_list, k = 2, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 3, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 4, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 5, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 6, fun = membership_heatmap, mc.cores = 4)
Signature heatmaps for all methods. (What is a signature heatmap?)
Note in following heatmaps, rows are scaled.
collect_plots(res_list, k = 2, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 3, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 4, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 5, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 6, fun = get_signatures, mc.cores = 4)
The statistics used for measuring the stability of consensus partitioning. (How are they defined?)
get_stats(res_list, k = 2)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 2 0.860 0.920 0.966 0.492 0.506 0.506
#> CV:NMF 2 0.815 0.883 0.953 0.496 0.500 0.500
#> MAD:NMF 2 0.893 0.927 0.969 0.493 0.503 0.503
#> ATC:NMF 2 0.964 0.951 0.980 0.500 0.499 0.499
#> SD:skmeans 2 0.940 0.944 0.977 0.503 0.498 0.498
#> CV:skmeans 2 0.917 0.925 0.970 0.503 0.497 0.497
#> MAD:skmeans 2 0.975 0.938 0.976 0.503 0.498 0.498
#> ATC:skmeans 2 1.000 0.970 0.988 0.503 0.497 0.497
#> SD:mclust 2 0.917 0.937 0.974 0.499 0.501 0.501
#> CV:mclust 2 0.320 0.758 0.857 0.210 0.922 0.922
#> MAD:mclust 2 0.872 0.917 0.966 0.497 0.502 0.502
#> ATC:mclust 2 0.462 0.857 0.903 0.416 0.602 0.602
#> SD:kmeans 2 0.777 0.895 0.954 0.493 0.502 0.502
#> CV:kmeans 2 0.722 0.883 0.944 0.496 0.497 0.497
#> MAD:kmeans 2 0.785 0.878 0.949 0.496 0.499 0.499
#> ATC:kmeans 2 0.905 0.924 0.970 0.496 0.502 0.502
#> SD:pam 2 0.895 0.945 0.976 0.412 0.582 0.582
#> CV:pam 2 0.515 0.850 0.904 0.393 0.613 0.613
#> MAD:pam 2 0.928 0.940 0.974 0.413 0.582 0.582
#> ATC:pam 2 0.810 0.903 0.956 0.410 0.568 0.568
#> SD:hclust 2 0.222 0.537 0.786 0.440 0.508 0.508
#> CV:hclust 2 0.135 0.609 0.755 0.414 0.497 0.497
#> MAD:hclust 2 0.280 0.649 0.825 0.442 0.525 0.525
#> ATC:hclust 2 0.406 0.736 0.871 0.422 0.556 0.556
get_stats(res_list, k = 3)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 3 0.624 0.702 0.813 0.337 0.749 0.541
#> CV:NMF 3 0.579 0.707 0.860 0.341 0.725 0.504
#> MAD:NMF 3 0.616 0.652 0.769 0.331 0.765 0.565
#> ATC:NMF 3 0.659 0.817 0.890 0.275 0.784 0.601
#> SD:skmeans 3 1.000 0.963 0.982 0.322 0.747 0.535
#> CV:skmeans 3 0.511 0.557 0.785 0.323 0.683 0.446
#> MAD:skmeans 3 1.000 0.959 0.983 0.320 0.748 0.536
#> ATC:skmeans 3 0.925 0.916 0.965 0.269 0.809 0.634
#> SD:mclust 3 0.504 0.639 0.796 0.269 0.783 0.589
#> CV:mclust 3 0.192 0.595 0.765 1.416 0.531 0.493
#> MAD:mclust 3 0.472 0.648 0.767 0.260 0.792 0.603
#> ATC:mclust 3 0.445 0.623 0.810 0.487 0.602 0.413
#> SD:kmeans 3 0.842 0.898 0.955 0.339 0.669 0.436
#> CV:kmeans 3 0.381 0.421 0.664 0.318 0.732 0.511
#> MAD:kmeans 3 0.835 0.874 0.945 0.333 0.671 0.435
#> ATC:kmeans 3 0.500 0.641 0.803 0.317 0.706 0.478
#> SD:pam 3 0.760 0.859 0.938 0.552 0.765 0.599
#> CV:pam 3 0.522 0.712 0.856 0.540 0.752 0.608
#> MAD:pam 3 0.779 0.874 0.945 0.569 0.767 0.600
#> ATC:pam 3 0.788 0.836 0.933 0.573 0.780 0.613
#> SD:hclust 3 0.262 0.436 0.686 0.338 0.667 0.456
#> CV:hclust 3 0.142 0.502 0.667 0.292 0.879 0.768
#> MAD:hclust 3 0.275 0.501 0.734 0.371 0.836 0.688
#> ATC:hclust 3 0.329 0.500 0.708 0.460 0.710 0.512
get_stats(res_list, k = 4)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 4 0.945 0.928 0.969 0.1406 0.861 0.617
#> CV:NMF 4 0.607 0.702 0.819 0.1153 0.797 0.492
#> MAD:NMF 4 0.921 0.913 0.962 0.1408 0.832 0.560
#> ATC:NMF 4 0.540 0.535 0.770 0.1364 0.896 0.727
#> SD:skmeans 4 0.968 0.932 0.971 0.1233 0.868 0.632
#> CV:skmeans 4 0.596 0.656 0.799 0.1254 0.804 0.493
#> MAD:skmeans 4 0.959 0.927 0.969 0.1230 0.868 0.634
#> ATC:skmeans 4 0.942 0.904 0.951 0.1474 0.845 0.602
#> SD:mclust 4 0.535 0.675 0.798 0.1586 0.813 0.515
#> CV:mclust 4 0.423 0.632 0.800 0.2664 0.858 0.710
#> MAD:mclust 4 0.719 0.774 0.883 0.1812 0.849 0.590
#> ATC:mclust 4 0.733 0.835 0.925 0.0697 0.785 0.528
#> SD:kmeans 4 0.907 0.917 0.963 0.1379 0.844 0.583
#> CV:kmeans 4 0.458 0.531 0.728 0.1224 0.819 0.524
#> MAD:kmeans 4 0.967 0.942 0.972 0.1346 0.864 0.624
#> ATC:kmeans 4 0.842 0.887 0.934 0.1305 0.807 0.508
#> SD:pam 4 0.768 0.801 0.915 0.1523 0.854 0.616
#> CV:pam 4 0.725 0.824 0.900 0.1800 0.851 0.644
#> MAD:pam 4 0.774 0.808 0.918 0.1457 0.851 0.606
#> ATC:pam 4 0.827 0.826 0.933 0.1289 0.852 0.614
#> SD:hclust 4 0.405 0.602 0.756 0.1949 0.752 0.437
#> CV:hclust 4 0.241 0.448 0.696 0.1645 0.740 0.517
#> MAD:hclust 4 0.416 0.588 0.759 0.1698 0.798 0.504
#> ATC:hclust 4 0.373 0.464 0.648 0.1446 0.794 0.493
get_stats(res_list, k = 5)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 5 0.796 0.692 0.838 0.0402 0.949 0.810
#> CV:NMF 5 0.742 0.742 0.859 0.0724 0.823 0.445
#> MAD:NMF 5 0.789 0.732 0.841 0.0419 0.937 0.763
#> ATC:NMF 5 0.655 0.673 0.812 0.0776 0.841 0.523
#> SD:skmeans 5 0.864 0.799 0.891 0.0496 0.940 0.773
#> CV:skmeans 5 0.806 0.759 0.888 0.0690 0.897 0.623
#> MAD:skmeans 5 0.879 0.832 0.908 0.0502 0.933 0.751
#> ATC:skmeans 5 0.798 0.694 0.860 0.0643 0.929 0.750
#> SD:mclust 5 0.786 0.842 0.895 0.0560 0.902 0.656
#> CV:mclust 5 0.431 0.542 0.727 0.1387 0.773 0.472
#> MAD:mclust 5 0.777 0.833 0.890 0.0537 0.893 0.629
#> ATC:mclust 5 0.607 0.580 0.793 0.1448 0.813 0.495
#> SD:kmeans 5 0.766 0.686 0.819 0.0490 0.978 0.914
#> CV:kmeans 5 0.557 0.517 0.696 0.0666 0.851 0.519
#> MAD:kmeans 5 0.769 0.681 0.807 0.0516 0.986 0.944
#> ATC:kmeans 5 0.708 0.626 0.809 0.0678 0.878 0.592
#> SD:pam 5 0.730 0.690 0.841 0.0404 0.946 0.806
#> CV:pam 5 0.800 0.837 0.910 0.0640 0.942 0.800
#> MAD:pam 5 0.727 0.670 0.852 0.0371 0.984 0.937
#> ATC:pam 5 0.797 0.804 0.902 0.0616 0.925 0.739
#> SD:hclust 5 0.474 0.542 0.734 0.0661 0.948 0.805
#> CV:hclust 5 0.312 0.478 0.660 0.1373 0.785 0.513
#> MAD:hclust 5 0.485 0.494 0.722 0.0639 0.935 0.761
#> ATC:hclust 5 0.469 0.463 0.666 0.0830 0.873 0.585
get_stats(res_list, k = 6)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 6 0.748 0.679 0.815 0.0360 0.948 0.788
#> CV:NMF 6 0.750 0.669 0.828 0.0399 0.916 0.635
#> MAD:NMF 6 0.738 0.660 0.807 0.0358 0.964 0.843
#> ATC:NMF 6 0.716 0.632 0.787 0.0331 0.946 0.769
#> SD:skmeans 6 0.767 0.662 0.794 0.0423 0.990 0.953
#> CV:skmeans 6 0.764 0.636 0.805 0.0362 0.931 0.686
#> MAD:skmeans 6 0.791 0.717 0.814 0.0414 0.975 0.886
#> ATC:skmeans 6 0.749 0.593 0.752 0.0408 0.924 0.697
#> SD:mclust 6 0.789 0.721 0.847 0.0408 0.905 0.639
#> CV:mclust 6 0.514 0.577 0.732 0.0630 0.924 0.720
#> MAD:mclust 6 0.760 0.720 0.853 0.0361 0.935 0.731
#> ATC:mclust 6 0.659 0.679 0.794 0.0625 0.837 0.412
#> SD:kmeans 6 0.723 0.620 0.756 0.0357 0.932 0.722
#> CV:kmeans 6 0.664 0.620 0.772 0.0427 0.895 0.590
#> MAD:kmeans 6 0.735 0.624 0.779 0.0350 0.924 0.696
#> ATC:kmeans 6 0.684 0.540 0.705 0.0417 0.899 0.580
#> SD:pam 6 0.746 0.692 0.858 0.0145 0.974 0.894
#> CV:pam 6 0.832 0.841 0.925 0.0211 0.993 0.971
#> MAD:pam 6 0.712 0.622 0.830 0.0194 0.975 0.901
#> ATC:pam 6 0.838 0.803 0.912 0.0409 0.959 0.826
#> SD:hclust 6 0.518 0.484 0.706 0.0351 0.966 0.859
#> CV:hclust 6 0.387 0.438 0.651 0.0626 0.949 0.826
#> MAD:hclust 6 0.531 0.476 0.698 0.0362 0.966 0.856
#> ATC:hclust 6 0.537 0.438 0.669 0.0332 0.951 0.794
Following heatmap plots the partition for each combination of methods and the lightness correspond to the silhouette scores for samples in each method. On top the consensus subgroup is inferred from all methods by taking the mean silhouette scores as weight.
collect_stats(res_list, k = 2)
collect_stats(res_list, k = 3)
collect_stats(res_list, k = 4)
collect_stats(res_list, k = 5)
collect_stats(res_list, k = 6)
Collect partitions from all methods:
collect_classes(res_list, k = 2)
collect_classes(res_list, k = 3)
collect_classes(res_list, k = 4)
collect_classes(res_list, k = 5)
collect_classes(res_list, k = 6)
Overlap of top rows from different top-row methods:
top_rows_overlap(res_list, top_n = 1000, method = "euler")
top_rows_overlap(res_list, top_n = 2000, method = "euler")
top_rows_overlap(res_list, top_n = 3000, method = "euler")
top_rows_overlap(res_list, top_n = 4000, method = "euler")
top_rows_overlap(res_list, top_n = 5000, method = "euler")
Also visualize the correspondance of rankings between different top-row methods:
top_rows_overlap(res_list, top_n = 1000, method = "correspondance")
top_rows_overlap(res_list, top_n = 2000, method = "correspondance")
top_rows_overlap(res_list, top_n = 3000, method = "correspondance")
top_rows_overlap(res_list, top_n = 4000, method = "correspondance")
top_rows_overlap(res_list, top_n = 5000, method = "correspondance")
Heatmaps of the top rows:
top_rows_heatmap(res_list, top_n = 1000)
top_rows_heatmap(res_list, top_n = 2000)
top_rows_heatmap(res_list, top_n = 3000)
top_rows_heatmap(res_list, top_n = 4000)
top_rows_heatmap(res_list, top_n = 5000)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res_list, k = 2)
#> n subtype(p) k
#> SD:NMF 167 2.11e-22 2
#> CV:NMF 159 1.46e-11 2
#> MAD:NMF 168 2.23e-22 2
#> ATC:NMF 170 6.82e-25 2
#> SD:skmeans 168 9.69e-23 2
#> CV:skmeans 165 1.05e-10 2
#> MAD:skmeans 167 2.00e-22 2
#> ATC:skmeans 169 2.19e-25 2
#> SD:mclust 166 2.09e-32 2
#> CV:mclust 160 5.17e-09 2
#> MAD:mclust 165 5.26e-33 2
#> ATC:mclust 169 4.46e-19 2
#> SD:kmeans 165 3.07e-22 2
#> CV:kmeans 167 5.46e-11 2
#> MAD:kmeans 163 4.75e-21 2
#> ATC:kmeans 167 5.56e-23 2
#> SD:pam 170 9.46e-28 2
#> CV:pam 171 1.79e-20 2
#> MAD:pam 169 1.80e-27 2
#> ATC:pam 159 1.03e-19 2
#> SD:hclust 110 5.73e-23 2
#> CV:hclust 141 9.18e-14 2
#> MAD:hclust 148 5.03e-30 2
#> ATC:hclust 153 1.32e-15 2
test_to_known_factors(res_list, k = 3)
#> n subtype(p) k
#> SD:NMF 152 1.54e-52 3
#> CV:NMF 147 8.46e-28 3
#> MAD:NMF 146 6.00e-51 3
#> ATC:NMF 166 4.07e-46 3
#> SD:skmeans 172 9.70e-57 3
#> CV:skmeans 132 6.87e-29 3
#> MAD:skmeans 169 1.15e-54 3
#> ATC:skmeans 166 7.60e-35 3
#> SD:mclust 134 1.60e-52 3
#> CV:mclust 143 2.26e-27 3
#> MAD:mclust 142 9.15e-56 3
#> ATC:mclust 130 1.36e-20 3
#> SD:kmeans 168 1.93e-50 3
#> CV:kmeans 49 NA 3
#> MAD:kmeans 162 3.81e-51 3
#> ATC:kmeans 137 8.71e-34 3
#> SD:pam 165 2.57e-38 3
#> CV:pam 157 5.09e-37 3
#> MAD:pam 163 1.65e-38 3
#> ATC:pam 153 2.03e-26 3
#> SD:hclust 84 1.19e-33 3
#> CV:hclust 102 1.33e-28 3
#> MAD:hclust 107 1.66e-42 3
#> ATC:hclust 94 9.77e-25 3
test_to_known_factors(res_list, k = 4)
#> n subtype(p) k
#> SD:NMF 169 1.15e-68 4
#> CV:NMF 150 3.61e-34 4
#> MAD:NMF 165 3.97e-72 4
#> ATC:NMF 106 1.24e-37 4
#> SD:skmeans 166 1.98e-81 4
#> CV:skmeans 137 1.85e-51 4
#> MAD:skmeans 165 1.92e-83 4
#> ATC:skmeans 167 1.49e-67 4
#> SD:mclust 140 8.88e-57 4
#> CV:mclust 147 9.18e-24 4
#> MAD:mclust 154 2.09e-64 4
#> ATC:mclust 167 4.43e-28 4
#> SD:kmeans 169 9.57e-73 4
#> CV:kmeans 118 9.00e-24 4
#> MAD:kmeans 172 1.94e-71 4
#> ATC:kmeans 170 6.65e-52 4
#> SD:pam 154 9.07e-55 4
#> CV:pam 162 7.74e-53 4
#> MAD:pam 157 8.88e-59 4
#> ATC:pam 155 6.43e-47 4
#> SD:hclust 132 1.20e-64 4
#> CV:hclust 72 6.22e-12 4
#> MAD:hclust 124 1.99e-66 4
#> ATC:hclust 74 1.09e-22 4
test_to_known_factors(res_list, k = 5)
#> n subtype(p) k
#> SD:NMF 132 6.25e-45 5
#> CV:NMF 150 6.42e-50 5
#> MAD:NMF 146 4.80e-78 5
#> ATC:NMF 143 1.26e-67 5
#> SD:skmeans 156 7.06e-84 5
#> CV:skmeans 148 1.97e-59 5
#> MAD:skmeans 159 7.03e-84 5
#> ATC:skmeans 132 1.52e-64 5
#> SD:mclust 164 1.22e-55 5
#> CV:mclust 116 1.54e-23 5
#> MAD:mclust 165 2.45e-58 5
#> ATC:mclust 117 2.20e-33 5
#> SD:kmeans 145 9.75e-69 5
#> CV:kmeans 85 4.64e-34 5
#> MAD:kmeans 142 6.37e-67 5
#> ATC:kmeans 126 3.67e-40 5
#> SD:pam 137 7.39e-50 5
#> CV:pam 164 2.78e-50 5
#> MAD:pam 137 1.90e-54 5
#> ATC:pam 157 1.29e-47 5
#> SD:hclust 120 3.81e-55 5
#> CV:hclust 92 1.78e-17 5
#> MAD:hclust 99 1.58e-48 5
#> ATC:hclust 92 2.49e-41 5
test_to_known_factors(res_list, k = 6)
#> n subtype(p) k
#> SD:NMF 145 4.24e-75 6
#> CV:NMF 141 1.77e-47 6
#> MAD:NMF 140 3.01e-75 6
#> ATC:NMF 132 7.69e-69 6
#> SD:skmeans 138 5.12e-76 6
#> CV:skmeans 126 1.53e-51 6
#> MAD:skmeans 150 2.72e-82 6
#> ATC:skmeans 113 7.19e-60 6
#> SD:mclust 146 1.89e-60 6
#> CV:mclust 135 4.29e-28 6
#> MAD:mclust 153 1.71e-61 6
#> ATC:mclust 145 2.19e-43 6
#> SD:kmeans 128 1.34e-67 6
#> CV:kmeans 138 2.36e-39 6
#> MAD:kmeans 131 1.42e-71 6
#> ATC:kmeans 119 5.32e-48 6
#> SD:pam 144 4.55e-53 6
#> CV:pam 163 4.18e-48 6
#> MAD:pam 127 1.60e-45 6
#> ATC:pam 156 1.36e-52 6
#> SD:hclust 102 2.12e-42 6
#> CV:hclust 79 4.46e-18 6
#> MAD:hclust 98 4.59e-48 6
#> ATC:hclust 85 1.28e-31 6
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "hclust"]
# you can also extract it by
# res = res_list["SD:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.222 0.537 0.786 0.4403 0.508 0.508
#> 3 3 0.262 0.436 0.686 0.3381 0.667 0.456
#> 4 4 0.405 0.602 0.756 0.1949 0.752 0.437
#> 5 5 0.474 0.542 0.734 0.0661 0.948 0.805
#> 6 6 0.518 0.484 0.706 0.0351 0.966 0.859
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.5294 0.7388 0.880 0.120
#> TCGA-02-0010-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.2603 0.7483 0.956 0.044
#> TCGA-02-0014-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.3431 0.7494 0.936 0.064
#> TCGA-02-0028-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.5294 0.7388 0.880 0.120
#> TCGA-02-0047-01A-01 1 0.9993 0.0846 0.516 0.484
#> TCGA-02-0048-01A-01 1 0.7219 0.6769 0.800 0.200
#> TCGA-02-0060-01A-01 1 0.6712 0.7117 0.824 0.176
#> TCGA-02-0069-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.5059 0.7430 0.888 0.112
#> TCGA-02-0080-01A-01 1 0.0376 0.7375 0.996 0.004
#> TCGA-02-0084-01A-03 1 0.8016 0.6121 0.756 0.244
#> TCGA-02-0087-01A-01 1 0.8016 0.6121 0.756 0.244
#> TCGA-02-0104-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.8861 0.5293 0.696 0.304
#> TCGA-02-0325-01A-01 1 0.8861 0.5293 0.696 0.304
#> TCGA-02-0338-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0376 0.7375 0.996 0.004
#> TCGA-02-0439-01A-01 1 0.8443 0.6107 0.728 0.272
#> TCGA-02-0440-01A-01 1 0.5842 0.7329 0.860 0.140
#> TCGA-02-0446-01A-01 1 0.9954 0.1679 0.540 0.460
#> TCGA-06-0128-01A-01 1 0.1633 0.7431 0.976 0.024
#> TCGA-06-0129-01A-01 1 0.0672 0.7389 0.992 0.008
#> TCGA-06-0146-01A-01 1 0.3114 0.7419 0.944 0.056
#> TCGA-06-0156-01A-01 1 0.9993 0.0868 0.516 0.484
#> TCGA-06-0166-01A-01 1 0.9795 0.3130 0.584 0.416
#> TCGA-06-0174-01A-01 1 0.5294 0.7388 0.880 0.120
#> TCGA-06-0177-01A-01 1 0.5294 0.7405 0.880 0.120
#> TCGA-06-0238-01A-02 1 0.5737 0.7345 0.864 0.136
#> TCGA-06-0241-01A-02 1 0.4939 0.7433 0.892 0.108
#> TCGA-06-0410-01A-01 1 0.4815 0.7445 0.896 0.104
#> TCGA-06-0413-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.5059 0.7430 0.888 0.112
#> TCGA-06-0646-01A-01 1 0.9998 0.0520 0.508 0.492
#> TCGA-06-0648-01A-01 1 0.3733 0.7497 0.928 0.072
#> TCGA-08-0245-01A-01 1 0.4431 0.7471 0.908 0.092
#> TCGA-08-0344-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.9954 0.1679 0.540 0.460
#> TCGA-08-0348-01A-01 1 0.7376 0.6847 0.792 0.208
#> TCGA-08-0350-01A-01 1 0.3733 0.7382 0.928 0.072
#> TCGA-08-0353-01A-01 1 0.9580 0.3158 0.620 0.380
#> TCGA-08-0359-01A-01 1 0.9686 0.3685 0.604 0.396
#> TCGA-08-0385-01A-01 1 0.2236 0.7431 0.964 0.036
#> TCGA-08-0517-01A-01 1 0.2948 0.7452 0.948 0.052
#> TCGA-08-0524-01A-01 1 0.0000 0.7358 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.5294 0.7415 0.880 0.120
#> TCGA-12-0618-01A-01 1 0.3431 0.7494 0.936 0.064
#> TCGA-02-0089-01A-01 2 0.9815 0.2926 0.420 0.580
#> TCGA-02-0113-01A-01 2 1.0000 0.1032 0.496 0.504
#> TCGA-02-0115-01A-01 1 0.9850 0.2377 0.572 0.428
#> TCGA-02-0451-01A-01 2 0.9795 0.2987 0.416 0.584
#> TCGA-06-0132-01A-02 1 0.9833 0.2489 0.576 0.424
#> TCGA-06-0133-01A-02 1 0.8661 0.5620 0.712 0.288
#> TCGA-06-0138-01A-02 1 0.9993 0.0180 0.516 0.484
#> TCGA-06-0160-01A-01 1 0.0376 0.7375 0.996 0.004
#> TCGA-06-0162-01A-01 1 0.8386 0.5837 0.732 0.268
#> TCGA-06-0167-01A-01 1 0.0376 0.7375 0.996 0.004
#> TCGA-06-0171-01A-02 1 0.9922 0.1892 0.552 0.448
#> TCGA-06-0173-01A-01 2 0.9393 0.4334 0.356 0.644
#> TCGA-06-0179-01A-02 1 0.9833 0.2489 0.576 0.424
#> TCGA-06-0182-01A-01 1 0.9954 0.0302 0.540 0.460
#> TCGA-06-0185-01A-01 2 0.9922 0.2907 0.448 0.552
#> TCGA-06-0195-01B-01 1 0.5629 0.7291 0.868 0.132
#> TCGA-06-0208-01B-01 1 0.8763 0.5489 0.704 0.296
#> TCGA-06-0214-01A-02 2 0.9833 0.2768 0.424 0.576
#> TCGA-06-0219-01A-01 1 0.7453 0.6584 0.788 0.212
#> TCGA-06-0221-01A-01 1 0.4161 0.7416 0.916 0.084
#> TCGA-06-0237-01A-02 1 0.9000 0.5151 0.684 0.316
#> TCGA-06-0240-01A-02 1 0.0376 0.7375 0.996 0.004
#> TCGA-08-0349-01A-01 1 0.9983 0.0817 0.524 0.476
#> TCGA-08-0380-01A-01 2 1.0000 0.0414 0.496 0.504
#> TCGA-08-0386-01A-01 1 0.9881 0.1636 0.564 0.436
#> TCGA-08-0520-01A-01 1 0.9933 0.1101 0.548 0.452
#> TCGA-02-0007-01A-01 1 0.9850 0.1708 0.572 0.428
#> TCGA-02-0009-01A-01 2 0.9909 0.3267 0.444 0.556
#> TCGA-02-0016-01A-01 2 0.9993 0.2081 0.484 0.516
#> TCGA-02-0021-01A-01 2 0.9922 0.3172 0.448 0.552
#> TCGA-02-0023-01B-01 2 0.8763 0.5479 0.296 0.704
#> TCGA-02-0027-01A-01 1 0.8763 0.5734 0.704 0.296
#> TCGA-02-0038-01A-01 2 0.9286 0.4578 0.344 0.656
#> TCGA-02-0043-01A-01 2 0.9922 0.3164 0.448 0.552
#> TCGA-02-0070-01A-01 2 0.3431 0.6766 0.064 0.936
#> TCGA-02-0102-01A-01 2 0.9909 0.3262 0.444 0.556
#> TCGA-02-0260-01A-03 2 0.9993 0.2229 0.484 0.516
#> TCGA-02-0269-01B-01 2 0.9993 0.2229 0.484 0.516
#> TCGA-02-0285-01A-01 2 0.9850 0.3611 0.428 0.572
#> TCGA-02-0289-01A-01 2 0.9922 0.3172 0.448 0.552
#> TCGA-02-0290-01A-01 2 0.9795 0.3783 0.416 0.584
#> TCGA-02-0317-01A-01 2 0.9993 0.2180 0.484 0.516
#> TCGA-02-0333-01A-02 2 0.9993 0.2229 0.484 0.516
#> TCGA-02-0422-01A-01 2 0.9795 0.3843 0.416 0.584
#> TCGA-02-0430-01A-01 2 0.9850 0.3611 0.428 0.572
#> TCGA-06-0125-01A-01 2 0.9909 0.3267 0.444 0.556
#> TCGA-06-0126-01A-01 2 0.9944 0.2948 0.456 0.544
#> TCGA-06-0137-01A-03 2 0.9954 0.2825 0.460 0.540
#> TCGA-06-0145-01A-04 2 0.9754 0.3985 0.408 0.592
#> TCGA-06-0148-01A-01 2 0.9850 0.3584 0.428 0.572
#> TCGA-06-0187-01A-01 2 0.9491 0.4599 0.368 0.632
#> TCGA-06-0211-01B-01 2 0.9944 0.2943 0.456 0.544
#> TCGA-06-0402-01A-01 2 0.9896 0.3360 0.440 0.560
#> TCGA-08-0246-01A-01 2 0.8499 0.5655 0.276 0.724
#> TCGA-08-0354-01A-01 2 0.8327 0.5775 0.264 0.736
#> TCGA-08-0355-01A-01 2 0.8443 0.5696 0.272 0.728
#> TCGA-08-0357-01A-01 2 0.9795 0.3843 0.416 0.584
#> TCGA-08-0358-01A-01 2 0.9993 0.2180 0.484 0.516
#> TCGA-08-0375-01A-01 2 0.9983 0.2457 0.476 0.524
#> TCGA-08-0511-01A-01 2 0.9427 0.4709 0.360 0.640
#> TCGA-08-0514-01A-01 2 0.9580 0.4426 0.380 0.620
#> TCGA-08-0518-01A-01 2 0.9881 0.3455 0.436 0.564
#> TCGA-08-0529-01A-02 2 0.9850 0.3611 0.428 0.572
#> TCGA-08-0531-01A-01 2 0.9881 0.3455 0.436 0.564
#> TCGA-02-0057-01A-01 2 0.9460 0.4233 0.364 0.636
#> TCGA-02-0004-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.9286 0.4502 0.344 0.656
#> TCGA-02-0025-01A-01 2 0.0376 0.6762 0.004 0.996
#> TCGA-02-0033-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0376 0.6782 0.004 0.996
#> TCGA-02-0039-01A-01 2 0.5178 0.6301 0.116 0.884
#> TCGA-02-0051-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.9248 0.4590 0.340 0.660
#> TCGA-02-0055-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0376 0.6782 0.004 0.996
#> TCGA-02-0079-01A-03 2 0.7950 0.5839 0.240 0.760
#> TCGA-02-0085-01A-01 2 0.9393 0.4163 0.356 0.644
#> TCGA-02-0086-01A-01 2 0.0672 0.6788 0.008 0.992
#> TCGA-02-0099-01A-01 2 0.9209 0.4632 0.336 0.664
#> TCGA-02-0106-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0672 0.6776 0.008 0.992
#> TCGA-02-0326-01A-01 2 0.9866 0.2941 0.432 0.568
#> TCGA-02-0337-01A-01 2 0.9286 0.4444 0.344 0.656
#> TCGA-06-0122-01A-01 2 0.3114 0.6779 0.056 0.944
#> TCGA-06-0124-01A-01 2 0.0376 0.6782 0.004 0.996
#> TCGA-06-0130-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.3584 0.6761 0.068 0.932
#> TCGA-06-0147-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.6438 0.6456 0.164 0.836
#> TCGA-06-0152-01A-02 2 0.9000 0.5262 0.316 0.684
#> TCGA-06-0154-01A-02 2 0.0938 0.6797 0.012 0.988
#> TCGA-06-0164-01A-01 2 0.0376 0.6781 0.004 0.996
#> TCGA-06-0175-01A-01 2 0.3733 0.6746 0.072 0.928
#> TCGA-06-0176-01A-03 2 0.0000 0.6767 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.8661 0.5265 0.288 0.712
#> TCGA-06-0189-01A-05 2 0.0000 0.6767 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0376 0.6782 0.004 0.996
#> TCGA-06-0194-01A-01 2 0.1184 0.6791 0.016 0.984
#> TCGA-06-0197-01A-02 2 0.0000 0.6767 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.2778 0.6787 0.048 0.952
#> TCGA-06-0397-01A-01 2 0.0376 0.6782 0.004 0.996
#> TCGA-06-0409-01A-02 2 0.0376 0.6762 0.004 0.996
#> TCGA-06-0412-01A-01 2 0.2778 0.6787 0.048 0.952
#> TCGA-06-0644-01A-02 2 0.0000 0.6767 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.2043 0.6740 0.032 0.968
#> TCGA-08-0346-01A-01 2 0.1633 0.6796 0.024 0.976
#> TCGA-08-0352-01A-01 2 0.6343 0.6454 0.160 0.840
#> TCGA-08-0360-01A-01 2 0.0672 0.6776 0.008 0.992
#> TCGA-08-0390-01A-01 2 0.6973 0.6009 0.188 0.812
#> TCGA-08-0392-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.5519 0.6300 0.128 0.872
#> TCGA-08-0510-01A-01 2 0.1184 0.6797 0.016 0.984
#> TCGA-08-0512-01A-01 2 0.0376 0.6782 0.004 0.996
#> TCGA-08-0522-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.6767 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.5294 0.6609 0.120 0.880
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.5138 0.5737 0.828 0.052 0.120
#> TCGA-02-0010-01A-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-02-0011-01B-01 1 0.5092 0.5122 0.804 0.020 0.176
#> TCGA-02-0014-01A-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-02-0024-01B-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-02-0026-01B-01 1 0.3802 0.5703 0.888 0.032 0.080
#> TCGA-02-0028-01A-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-02-0046-01A-01 1 0.5138 0.5737 0.828 0.052 0.120
#> TCGA-02-0047-01A-01 3 0.9433 0.3285 0.176 0.404 0.420
#> TCGA-02-0048-01A-01 1 0.6663 0.5549 0.748 0.096 0.156
#> TCGA-02-0060-01A-01 1 0.8494 0.2542 0.556 0.108 0.336
#> TCGA-02-0069-01A-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-02-0074-01A-01 1 0.4892 0.5731 0.840 0.048 0.112
#> TCGA-02-0080-01A-01 1 0.4465 0.4605 0.820 0.004 0.176
#> TCGA-02-0084-01A-03 1 0.9546 0.0943 0.472 0.216 0.312
#> TCGA-02-0087-01A-01 1 0.9546 0.0943 0.472 0.216 0.312
#> TCGA-02-0104-01A-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-02-0114-01A-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-02-0281-01A-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-02-0321-01A-01 1 0.9025 0.4108 0.544 0.172 0.284
#> TCGA-02-0325-01A-01 1 0.9025 0.4108 0.544 0.172 0.284
#> TCGA-02-0338-01A-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-02-0339-01A-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-02-0432-01A-02 1 0.4465 0.4605 0.820 0.004 0.176
#> TCGA-02-0439-01A-01 1 0.9690 -0.1309 0.424 0.220 0.356
#> TCGA-02-0440-01A-01 1 0.5851 0.5588 0.792 0.068 0.140
#> TCGA-02-0446-01A-01 3 0.9715 0.3534 0.220 0.380 0.400
#> TCGA-06-0128-01A-01 1 0.5171 0.4476 0.784 0.012 0.204
#> TCGA-06-0129-01A-01 1 0.3983 0.4863 0.852 0.004 0.144
#> TCGA-06-0146-01A-01 1 0.5956 0.4650 0.768 0.044 0.188
#> TCGA-06-0156-01A-01 2 0.9522 -0.3533 0.188 0.408 0.404
#> TCGA-06-0166-01A-01 2 1.0000 -0.3655 0.332 0.336 0.332
#> TCGA-06-0174-01A-01 1 0.5138 0.5737 0.828 0.052 0.120
#> TCGA-06-0177-01A-01 1 0.5891 0.5385 0.780 0.052 0.168
#> TCGA-06-0238-01A-02 1 0.6372 0.5305 0.756 0.068 0.176
#> TCGA-06-0241-01A-02 1 0.4443 0.5799 0.864 0.052 0.084
#> TCGA-06-0410-01A-01 1 0.4253 0.5804 0.872 0.048 0.080
#> TCGA-06-0413-01A-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-06-0414-01A-01 1 0.4786 0.5749 0.844 0.044 0.112
#> TCGA-06-0646-01A-01 2 0.9464 -0.3454 0.180 0.412 0.408
#> TCGA-06-0648-01A-01 1 0.4137 0.5700 0.872 0.032 0.096
#> TCGA-08-0245-01A-01 1 0.3764 0.5801 0.892 0.040 0.068
#> TCGA-08-0344-01A-01 1 0.1411 0.5404 0.964 0.000 0.036
#> TCGA-08-0347-01A-01 3 0.9715 0.3534 0.220 0.380 0.400
#> TCGA-08-0348-01A-01 1 0.8801 0.2305 0.560 0.148 0.292
#> TCGA-08-0350-01A-01 1 0.6447 0.4574 0.744 0.060 0.196
#> TCGA-08-0353-01A-01 1 0.8595 0.5153 0.604 0.216 0.180
#> TCGA-08-0359-01A-01 3 0.9865 0.4088 0.268 0.324 0.408
#> TCGA-08-0385-01A-01 1 0.2564 0.5556 0.936 0.028 0.036
#> TCGA-08-0517-01A-01 1 0.3155 0.5682 0.916 0.040 0.044
#> TCGA-08-0524-01A-01 1 0.0747 0.5459 0.984 0.000 0.016
#> TCGA-12-0616-01A-01 1 0.4902 0.5796 0.844 0.064 0.092
#> TCGA-12-0618-01A-01 1 0.3889 0.5690 0.884 0.032 0.084
#> TCGA-02-0089-01A-01 2 0.6825 -0.1452 0.012 0.496 0.492
#> TCGA-02-0113-01A-01 3 0.9887 0.0822 0.268 0.336 0.396
#> TCGA-02-0115-01A-01 3 0.5905 0.4420 0.000 0.352 0.648
#> TCGA-02-0451-01A-01 2 0.7395 -0.1546 0.032 0.492 0.476
#> TCGA-06-0132-01A-02 3 0.5882 0.4461 0.000 0.348 0.652
#> TCGA-06-0133-01A-02 3 0.7179 0.5885 0.104 0.184 0.712
#> TCGA-06-0138-01A-02 3 0.7546 0.3736 0.044 0.396 0.560
#> TCGA-06-0160-01A-01 3 0.4887 0.4451 0.228 0.000 0.772
#> TCGA-06-0162-01A-01 3 0.5435 0.5539 0.024 0.192 0.784
#> TCGA-06-0167-01A-01 3 0.4887 0.4451 0.228 0.000 0.772
#> TCGA-06-0171-01A-02 3 0.7600 0.4710 0.056 0.344 0.600
#> TCGA-06-0173-01A-01 2 0.6848 0.0984 0.016 0.568 0.416
#> TCGA-06-0179-01A-02 3 0.5882 0.4461 0.000 0.348 0.652
#> TCGA-06-0182-01A-01 3 0.8795 0.2968 0.168 0.256 0.576
#> TCGA-06-0185-01A-01 2 0.9858 -0.0898 0.252 0.376 0.372
#> TCGA-06-0195-01B-01 3 0.6544 0.5451 0.164 0.084 0.752
#> TCGA-06-0208-01B-01 3 0.7447 0.5825 0.120 0.184 0.696
#> TCGA-06-0214-01A-02 2 0.7839 -0.1662 0.052 0.484 0.464
#> TCGA-06-0219-01A-01 3 0.5780 0.5885 0.080 0.120 0.800
#> TCGA-06-0221-01A-01 3 0.7062 0.4972 0.236 0.068 0.696
#> TCGA-06-0237-01A-02 3 0.7368 0.5817 0.104 0.200 0.696
#> TCGA-06-0240-01A-02 3 0.4887 0.4451 0.228 0.000 0.772
#> TCGA-08-0349-01A-01 3 0.8573 0.4132 0.104 0.372 0.524
#> TCGA-08-0380-01A-01 3 0.6215 0.3060 0.000 0.428 0.572
#> TCGA-08-0386-01A-01 3 0.9914 -0.0298 0.328 0.280 0.392
#> TCGA-08-0520-01A-01 3 0.9768 0.1792 0.264 0.296 0.440
#> TCGA-02-0007-01A-01 1 0.9850 0.2228 0.392 0.252 0.356
#> TCGA-02-0009-01A-01 1 0.9674 0.4479 0.440 0.336 0.224
#> TCGA-02-0016-01A-01 1 0.9746 0.4271 0.436 0.320 0.244
#> TCGA-02-0021-01A-01 1 0.9664 0.4524 0.444 0.332 0.224
#> TCGA-02-0023-01B-01 2 0.9268 0.1272 0.268 0.524 0.208
#> TCGA-02-0027-01A-01 1 0.9546 0.1750 0.472 0.216 0.312
#> TCGA-02-0038-01A-01 2 0.6811 0.1353 0.016 0.580 0.404
#> TCGA-02-0043-01A-01 1 0.9664 0.4526 0.444 0.332 0.224
#> TCGA-02-0070-01A-01 2 0.4966 0.6088 0.060 0.840 0.100
#> TCGA-02-0102-01A-01 1 0.9625 0.4369 0.440 0.348 0.212
#> TCGA-02-0260-01A-03 1 0.9565 0.4716 0.476 0.296 0.228
#> TCGA-02-0269-01B-01 1 0.9565 0.4716 0.476 0.296 0.228
#> TCGA-02-0285-01A-01 1 0.9642 0.3823 0.416 0.376 0.208
#> TCGA-02-0289-01A-01 1 0.9664 0.4524 0.444 0.332 0.224
#> TCGA-02-0290-01A-01 1 0.9620 0.3846 0.416 0.380 0.204
#> TCGA-02-0317-01A-01 1 0.9616 0.4657 0.468 0.296 0.236
#> TCGA-02-0333-01A-02 1 0.9565 0.4716 0.476 0.296 0.228
#> TCGA-02-0422-01A-01 1 0.9673 0.3522 0.400 0.388 0.212
#> TCGA-02-0430-01A-01 1 0.9642 0.3823 0.416 0.376 0.208
#> TCGA-06-0125-01A-01 1 0.9674 0.4479 0.440 0.336 0.224
#> TCGA-06-0126-01A-01 1 0.9639 0.4566 0.448 0.332 0.220
#> TCGA-06-0137-01A-03 1 0.9649 0.4462 0.444 0.336 0.220
#> TCGA-06-0145-01A-04 1 0.9713 0.3758 0.404 0.376 0.220
#> TCGA-06-0148-01A-01 1 0.9672 0.4165 0.424 0.360 0.216
#> TCGA-06-0187-01A-01 2 0.9442 -0.1911 0.360 0.456 0.184
#> TCGA-06-0211-01B-01 1 0.9833 0.4200 0.412 0.332 0.256
#> TCGA-06-0402-01A-01 1 0.9684 0.4419 0.436 0.340 0.224
#> TCGA-08-0246-01A-01 2 0.9007 0.1716 0.268 0.552 0.180
#> TCGA-08-0354-01A-01 2 0.9110 0.1541 0.260 0.544 0.196
#> TCGA-08-0355-01A-01 2 0.9006 0.2071 0.256 0.556 0.188
#> TCGA-08-0357-01A-01 1 0.9673 0.3522 0.400 0.388 0.212
#> TCGA-08-0358-01A-01 1 0.9616 0.4657 0.468 0.296 0.236
#> TCGA-08-0375-01A-01 1 0.9598 0.4664 0.468 0.304 0.228
#> TCGA-08-0511-01A-01 2 0.9229 -0.0997 0.348 0.488 0.164
#> TCGA-08-0514-01A-01 2 0.9439 -0.2355 0.376 0.444 0.180
#> TCGA-08-0518-01A-01 1 0.9692 0.4357 0.432 0.344 0.224
#> TCGA-08-0529-01A-02 1 0.9642 0.3823 0.416 0.376 0.208
#> TCGA-08-0531-01A-01 1 0.9692 0.4357 0.432 0.344 0.224
#> TCGA-02-0057-01A-01 2 0.6598 0.0810 0.008 0.564 0.428
#> TCGA-02-0004-01A-01 2 0.0424 0.6830 0.000 0.992 0.008
#> TCGA-02-0006-01B-01 2 0.6688 0.1274 0.012 0.580 0.408
#> TCGA-02-0025-01A-01 2 0.0424 0.6834 0.000 0.992 0.008
#> TCGA-02-0033-01A-01 2 0.0237 0.6842 0.000 0.996 0.004
#> TCGA-02-0034-01A-01 2 0.0829 0.6867 0.004 0.984 0.012
#> TCGA-02-0039-01A-01 2 0.4629 0.5631 0.004 0.808 0.188
#> TCGA-02-0051-01A-01 2 0.0237 0.6842 0.000 0.996 0.004
#> TCGA-02-0054-01A-01 2 0.6675 0.1404 0.012 0.584 0.404
#> TCGA-02-0055-01A-01 2 0.0424 0.6830 0.000 0.992 0.008
#> TCGA-02-0059-01A-01 2 0.0237 0.6842 0.000 0.996 0.004
#> TCGA-02-0064-01A-01 2 0.0237 0.6840 0.000 0.996 0.004
#> TCGA-02-0075-01A-01 2 0.0661 0.6867 0.004 0.988 0.008
#> TCGA-02-0079-01A-03 2 0.6653 0.4050 0.032 0.680 0.288
#> TCGA-02-0085-01A-01 2 0.6577 0.0712 0.008 0.572 0.420
#> TCGA-02-0086-01A-01 2 0.2063 0.6772 0.008 0.948 0.044
#> TCGA-02-0099-01A-01 2 0.6661 0.1498 0.012 0.588 0.400
#> TCGA-02-0106-01A-01 2 0.0237 0.6842 0.000 0.996 0.004
#> TCGA-02-0107-01A-01 2 0.0592 0.6818 0.000 0.988 0.012
#> TCGA-02-0111-01A-01 2 0.1031 0.6823 0.000 0.976 0.024
#> TCGA-02-0326-01A-01 2 0.9658 -0.0969 0.212 0.420 0.368
#> TCGA-02-0337-01A-01 2 0.6910 0.1242 0.020 0.584 0.396
#> TCGA-06-0122-01A-01 2 0.4095 0.6393 0.056 0.880 0.064
#> TCGA-06-0124-01A-01 2 0.1129 0.6853 0.004 0.976 0.020
#> TCGA-06-0130-01A-01 2 0.0424 0.6830 0.000 0.992 0.008
#> TCGA-06-0139-01A-01 2 0.0424 0.6830 0.000 0.992 0.008
#> TCGA-06-0143-01A-01 2 0.4379 0.6340 0.060 0.868 0.072
#> TCGA-06-0147-01A-01 2 0.0424 0.6830 0.000 0.992 0.008
#> TCGA-06-0149-01A-05 2 0.6793 0.5143 0.128 0.744 0.128
#> TCGA-06-0152-01A-02 2 0.9491 -0.0158 0.292 0.488 0.220
#> TCGA-06-0154-01A-02 2 0.1877 0.6813 0.012 0.956 0.032
#> TCGA-06-0164-01A-01 2 0.0747 0.6837 0.000 0.984 0.016
#> TCGA-06-0175-01A-01 2 0.4397 0.6420 0.028 0.856 0.116
#> TCGA-06-0176-01A-03 2 0.0424 0.6830 0.000 0.992 0.008
#> TCGA-06-0184-01A-01 2 0.5882 0.3084 0.000 0.652 0.348
#> TCGA-06-0189-01A-05 2 0.0424 0.6857 0.000 0.992 0.008
#> TCGA-06-0190-01A-01 2 0.1129 0.6853 0.004 0.976 0.020
#> TCGA-06-0194-01A-01 2 0.1832 0.6830 0.008 0.956 0.036
#> TCGA-06-0197-01A-02 2 0.0237 0.6842 0.000 0.996 0.004
#> TCGA-06-0210-01A-01 2 0.3983 0.6425 0.048 0.884 0.068
#> TCGA-06-0397-01A-01 2 0.1015 0.6844 0.008 0.980 0.012
#> TCGA-06-0409-01A-02 2 0.0592 0.6818 0.000 0.988 0.012
#> TCGA-06-0412-01A-01 2 0.3983 0.6425 0.048 0.884 0.068
#> TCGA-06-0644-01A-02 2 0.0237 0.6842 0.000 0.996 0.004
#> TCGA-06-0645-01A-01 2 0.2448 0.6736 0.000 0.924 0.076
#> TCGA-08-0346-01A-01 2 0.2269 0.6799 0.016 0.944 0.040
#> TCGA-08-0352-01A-01 2 0.6981 0.4893 0.132 0.732 0.136
#> TCGA-08-0360-01A-01 2 0.1129 0.6859 0.004 0.976 0.020
#> TCGA-08-0390-01A-01 2 0.5216 0.4624 0.000 0.740 0.260
#> TCGA-08-0392-01A-01 2 0.0237 0.6842 0.000 0.996 0.004
#> TCGA-08-0509-01A-01 2 0.4555 0.5446 0.000 0.800 0.200
#> TCGA-08-0510-01A-01 2 0.2998 0.6629 0.016 0.916 0.068
#> TCGA-08-0512-01A-01 2 0.0237 0.6855 0.004 0.996 0.000
#> TCGA-08-0522-01A-01 2 0.0237 0.6842 0.000 0.996 0.004
#> TCGA-12-0619-01A-01 2 0.0747 0.6866 0.000 0.984 0.016
#> TCGA-12-0620-01A-01 2 0.6031 0.5478 0.116 0.788 0.096
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.6131 0.7081 0.680 0.008 0.224 0.088
#> TCGA-02-0010-01A-01 1 0.0469 0.7606 0.988 0.000 0.012 0.000
#> TCGA-02-0011-01B-01 1 0.6805 0.6804 0.604 0.000 0.220 0.176
#> TCGA-02-0014-01A-01 1 0.0469 0.7606 0.988 0.000 0.012 0.000
#> TCGA-02-0024-01B-01 1 0.0469 0.7606 0.988 0.000 0.012 0.000
#> TCGA-02-0026-01B-01 1 0.5172 0.7614 0.744 0.000 0.188 0.068
#> TCGA-02-0028-01A-01 1 0.0469 0.7606 0.988 0.000 0.012 0.000
#> TCGA-02-0046-01A-01 1 0.6131 0.7081 0.680 0.008 0.224 0.088
#> TCGA-02-0047-01A-01 4 0.9137 0.5702 0.100 0.260 0.204 0.436
#> TCGA-02-0048-01A-01 1 0.6553 0.5239 0.572 0.008 0.352 0.068
#> TCGA-02-0060-01A-01 4 0.9034 -0.2043 0.320 0.056 0.300 0.324
#> TCGA-02-0069-01A-01 1 0.0469 0.7606 0.988 0.000 0.012 0.000
#> TCGA-02-0074-01A-01 1 0.6251 0.7091 0.668 0.008 0.232 0.092
#> TCGA-02-0080-01A-01 1 0.5963 0.6961 0.688 0.000 0.116 0.196
#> TCGA-02-0084-01A-03 3 0.9034 -0.0423 0.240 0.064 0.364 0.332
#> TCGA-02-0087-01A-01 3 0.9034 -0.0423 0.240 0.064 0.364 0.332
#> TCGA-02-0104-01A-01 1 0.0657 0.7597 0.984 0.000 0.012 0.004
#> TCGA-02-0114-01A-01 1 0.0469 0.7606 0.988 0.000 0.012 0.000
#> TCGA-02-0281-01A-01 1 0.0469 0.7606 0.988 0.000 0.012 0.000
#> TCGA-02-0321-01A-01 3 0.7801 0.1098 0.272 0.012 0.504 0.212
#> TCGA-02-0325-01A-01 3 0.7801 0.1098 0.272 0.012 0.504 0.212
#> TCGA-02-0338-01A-01 1 0.0469 0.7606 0.988 0.000 0.012 0.000
#> TCGA-02-0339-01A-01 1 0.0469 0.7606 0.988 0.000 0.012 0.000
#> TCGA-02-0432-01A-02 1 0.5963 0.6961 0.688 0.000 0.116 0.196
#> TCGA-02-0439-01A-01 4 0.9483 0.1869 0.260 0.108 0.280 0.352
#> TCGA-02-0440-01A-01 1 0.6806 0.6658 0.620 0.012 0.256 0.112
#> TCGA-02-0446-01A-01 4 0.9427 0.5603 0.140 0.240 0.204 0.416
#> TCGA-06-0128-01A-01 1 0.6178 0.6647 0.660 0.000 0.112 0.228
#> TCGA-06-0129-01A-01 1 0.5280 0.7272 0.748 0.000 0.096 0.156
#> TCGA-06-0146-01A-01 1 0.7117 0.6150 0.584 0.004 0.196 0.216
#> TCGA-06-0156-01A-01 4 0.9312 0.5650 0.120 0.260 0.200 0.420
#> TCGA-06-0166-01A-01 4 0.9816 0.4252 0.232 0.196 0.224 0.348
#> TCGA-06-0174-01A-01 1 0.6131 0.7081 0.680 0.008 0.224 0.088
#> TCGA-06-0177-01A-01 1 0.7164 0.6157 0.552 0.004 0.296 0.148
#> TCGA-06-0238-01A-02 1 0.7367 0.5599 0.516 0.004 0.320 0.160
#> TCGA-06-0241-01A-02 1 0.5305 0.7309 0.732 0.008 0.216 0.044
#> TCGA-06-0410-01A-01 1 0.5326 0.7282 0.724 0.008 0.228 0.040
#> TCGA-06-0413-01A-01 1 0.0469 0.7606 0.988 0.000 0.012 0.000
#> TCGA-06-0414-01A-01 1 0.6010 0.7217 0.688 0.008 0.224 0.080
#> TCGA-06-0646-01A-01 4 0.9251 0.5643 0.112 0.264 0.200 0.424
#> TCGA-06-0648-01A-01 1 0.5548 0.7512 0.716 0.000 0.200 0.084
#> TCGA-08-0245-01A-01 1 0.4781 0.7473 0.772 0.008 0.188 0.032
#> TCGA-08-0344-01A-01 1 0.2214 0.7621 0.928 0.000 0.044 0.028
#> TCGA-08-0347-01A-01 4 0.9427 0.5603 0.140 0.240 0.204 0.416
#> TCGA-08-0348-01A-01 1 0.9259 0.1702 0.356 0.080 0.288 0.276
#> TCGA-08-0350-01A-01 1 0.7397 0.5653 0.544 0.004 0.228 0.224
#> TCGA-08-0353-01A-01 3 0.5143 0.4520 0.264 0.008 0.708 0.020
#> TCGA-08-0359-01A-01 4 0.9419 0.5085 0.160 0.188 0.224 0.428
#> TCGA-08-0385-01A-01 1 0.4365 0.7507 0.784 0.000 0.188 0.028
#> TCGA-08-0517-01A-01 1 0.3607 0.7724 0.864 0.008 0.096 0.032
#> TCGA-08-0524-01A-01 1 0.0469 0.7606 0.988 0.000 0.012 0.000
#> TCGA-12-0616-01A-01 1 0.6007 0.6188 0.604 0.000 0.340 0.056
#> TCGA-12-0618-01A-01 1 0.5384 0.7550 0.728 0.000 0.196 0.076
#> TCGA-02-0089-01A-01 4 0.6714 0.4976 0.000 0.360 0.100 0.540
#> TCGA-02-0113-01A-01 3 0.7014 0.4176 0.020 0.104 0.604 0.272
#> TCGA-02-0115-01A-01 4 0.4635 0.5823 0.000 0.268 0.012 0.720
#> TCGA-02-0451-01A-01 4 0.6949 0.5180 0.000 0.348 0.124 0.528
#> TCGA-06-0132-01A-02 4 0.4511 0.5803 0.000 0.268 0.008 0.724
#> TCGA-06-0133-01A-02 4 0.5858 0.5195 0.012 0.088 0.180 0.720
#> TCGA-06-0138-01A-02 4 0.6785 0.5966 0.008 0.264 0.116 0.612
#> TCGA-06-0160-01A-01 4 0.3450 0.3407 0.156 0.000 0.008 0.836
#> TCGA-06-0162-01A-01 4 0.3464 0.5952 0.004 0.124 0.016 0.856
#> TCGA-06-0167-01A-01 4 0.3450 0.3407 0.156 0.000 0.008 0.836
#> TCGA-06-0171-01A-02 4 0.7030 0.6216 0.012 0.208 0.164 0.616
#> TCGA-06-0173-01A-01 4 0.6785 0.3933 0.000 0.420 0.096 0.484
#> TCGA-06-0179-01A-02 4 0.4511 0.5803 0.000 0.268 0.008 0.724
#> TCGA-06-0182-01A-01 3 0.6223 0.2770 0.000 0.060 0.556 0.384
#> TCGA-06-0185-01A-01 3 0.6355 0.5502 0.008 0.104 0.664 0.224
#> TCGA-06-0195-01B-01 4 0.5403 0.4824 0.104 0.056 0.056 0.784
#> TCGA-06-0208-01B-01 4 0.5988 0.5000 0.012 0.084 0.200 0.704
#> TCGA-06-0214-01A-02 4 0.7507 0.5198 0.012 0.344 0.140 0.504
#> TCGA-06-0219-01A-01 4 0.4339 0.5548 0.024 0.068 0.068 0.840
#> TCGA-06-0221-01A-01 4 0.6006 0.4112 0.180 0.056 0.040 0.724
#> TCGA-06-0237-01A-02 4 0.6277 0.5212 0.012 0.104 0.200 0.684
#> TCGA-06-0240-01A-02 4 0.3450 0.3407 0.156 0.000 0.008 0.836
#> TCGA-08-0349-01A-01 4 0.7672 0.5837 0.016 0.216 0.224 0.544
#> TCGA-08-0380-01A-01 4 0.5712 0.5619 0.000 0.308 0.048 0.644
#> TCGA-08-0386-01A-01 3 0.7432 0.4000 0.064 0.068 0.584 0.284
#> TCGA-08-0520-01A-01 3 0.7272 0.2978 0.028 0.088 0.552 0.332
#> TCGA-02-0007-01A-01 3 0.6642 0.5382 0.072 0.040 0.668 0.220
#> TCGA-02-0009-01A-01 3 0.1174 0.7710 0.012 0.020 0.968 0.000
#> TCGA-02-0016-01A-01 3 0.3423 0.7557 0.028 0.024 0.884 0.064
#> TCGA-02-0021-01A-01 3 0.1059 0.7694 0.012 0.016 0.972 0.000
#> TCGA-02-0023-01B-01 3 0.5733 0.5541 0.008 0.240 0.696 0.056
#> TCGA-02-0027-01A-01 3 0.8981 0.0963 0.196 0.080 0.428 0.296
#> TCGA-02-0038-01A-01 4 0.7076 0.3816 0.000 0.416 0.124 0.460
#> TCGA-02-0043-01A-01 3 0.1059 0.7692 0.012 0.016 0.972 0.000
#> TCGA-02-0070-01A-01 2 0.5773 0.4766 0.000 0.620 0.336 0.044
#> TCGA-02-0102-01A-01 3 0.1639 0.7729 0.008 0.036 0.952 0.004
#> TCGA-02-0260-01A-03 3 0.1389 0.7565 0.048 0.000 0.952 0.000
#> TCGA-02-0269-01B-01 3 0.1389 0.7565 0.048 0.000 0.952 0.000
#> TCGA-02-0285-01A-01 3 0.3182 0.7621 0.012 0.064 0.892 0.032
#> TCGA-02-0289-01A-01 3 0.1247 0.7706 0.012 0.016 0.968 0.004
#> TCGA-02-0290-01A-01 3 0.2635 0.7653 0.016 0.072 0.908 0.004
#> TCGA-02-0317-01A-01 3 0.1807 0.7517 0.052 0.000 0.940 0.008
#> TCGA-02-0333-01A-02 3 0.1389 0.7565 0.048 0.000 0.952 0.000
#> TCGA-02-0422-01A-01 3 0.3902 0.7505 0.024 0.080 0.860 0.036
#> TCGA-02-0430-01A-01 3 0.3182 0.7621 0.012 0.064 0.892 0.032
#> TCGA-06-0125-01A-01 3 0.1174 0.7710 0.012 0.020 0.968 0.000
#> TCGA-06-0126-01A-01 3 0.1958 0.7710 0.028 0.020 0.944 0.008
#> TCGA-06-0137-01A-03 3 0.2424 0.7693 0.020 0.020 0.928 0.032
#> TCGA-06-0145-01A-04 3 0.2075 0.7694 0.004 0.044 0.936 0.016
#> TCGA-06-0148-01A-01 3 0.1938 0.7715 0.012 0.052 0.936 0.000
#> TCGA-06-0187-01A-01 3 0.4282 0.6915 0.004 0.148 0.812 0.036
#> TCGA-06-0211-01B-01 3 0.3017 0.7677 0.028 0.024 0.904 0.044
#> TCGA-06-0402-01A-01 3 0.1229 0.7715 0.008 0.020 0.968 0.004
#> TCGA-08-0246-01A-01 3 0.5472 0.4965 0.000 0.280 0.676 0.044
#> TCGA-08-0354-01A-01 3 0.5112 0.5633 0.004 0.252 0.716 0.028
#> TCGA-08-0355-01A-01 3 0.5574 0.4839 0.000 0.284 0.668 0.048
#> TCGA-08-0357-01A-01 3 0.3902 0.7505 0.024 0.080 0.860 0.036
#> TCGA-08-0358-01A-01 3 0.1807 0.7517 0.052 0.000 0.940 0.008
#> TCGA-08-0375-01A-01 3 0.1389 0.7551 0.048 0.000 0.952 0.000
#> TCGA-08-0511-01A-01 3 0.5076 0.6419 0.000 0.172 0.756 0.072
#> TCGA-08-0514-01A-01 3 0.4038 0.7084 0.004 0.136 0.828 0.032
#> TCGA-08-0518-01A-01 3 0.1584 0.7730 0.012 0.036 0.952 0.000
#> TCGA-08-0529-01A-02 3 0.3182 0.7621 0.012 0.064 0.892 0.032
#> TCGA-08-0531-01A-01 3 0.1575 0.7732 0.012 0.028 0.956 0.004
#> TCGA-02-0057-01A-01 4 0.6733 0.3993 0.000 0.416 0.092 0.492
#> TCGA-02-0004-01A-01 2 0.0779 0.7724 0.000 0.980 0.004 0.016
#> TCGA-02-0006-01B-01 4 0.6748 0.3707 0.000 0.432 0.092 0.476
#> TCGA-02-0025-01A-01 2 0.1892 0.7658 0.004 0.944 0.036 0.016
#> TCGA-02-0033-01A-01 2 0.0336 0.7785 0.000 0.992 0.008 0.000
#> TCGA-02-0034-01A-01 2 0.1733 0.7819 0.000 0.948 0.028 0.024
#> TCGA-02-0039-01A-01 2 0.6112 0.4233 0.000 0.656 0.096 0.248
#> TCGA-02-0051-01A-01 2 0.0927 0.7738 0.000 0.976 0.008 0.016
#> TCGA-02-0054-01A-01 4 0.6752 0.3519 0.000 0.440 0.092 0.468
#> TCGA-02-0055-01A-01 2 0.0779 0.7724 0.000 0.980 0.004 0.016
#> TCGA-02-0059-01A-01 2 0.0336 0.7785 0.000 0.992 0.008 0.000
#> TCGA-02-0064-01A-01 2 0.1576 0.7787 0.000 0.948 0.048 0.004
#> TCGA-02-0075-01A-01 2 0.2402 0.7686 0.000 0.912 0.076 0.012
#> TCGA-02-0079-01A-03 2 0.7748 -0.1436 0.004 0.452 0.208 0.336
#> TCGA-02-0085-01A-01 4 0.6546 0.3620 0.000 0.432 0.076 0.492
#> TCGA-02-0086-01A-01 2 0.3485 0.7403 0.000 0.856 0.116 0.028
#> TCGA-02-0099-01A-01 4 0.6707 0.3445 0.000 0.444 0.088 0.468
#> TCGA-02-0106-01A-01 2 0.1182 0.7774 0.000 0.968 0.016 0.016
#> TCGA-02-0107-01A-01 2 0.0376 0.7747 0.000 0.992 0.004 0.004
#> TCGA-02-0111-01A-01 2 0.1174 0.7786 0.000 0.968 0.020 0.012
#> TCGA-02-0326-01A-01 3 0.7938 0.2290 0.032 0.180 0.536 0.252
#> TCGA-02-0337-01A-01 2 0.7134 -0.3439 0.008 0.452 0.100 0.440
#> TCGA-06-0122-01A-01 2 0.5574 0.5507 0.000 0.668 0.284 0.048
#> TCGA-06-0124-01A-01 2 0.2662 0.7623 0.000 0.900 0.084 0.016
#> TCGA-06-0130-01A-01 2 0.0779 0.7724 0.000 0.980 0.004 0.016
#> TCGA-06-0139-01A-01 2 0.0188 0.7766 0.000 0.996 0.004 0.000
#> TCGA-06-0143-01A-01 2 0.5745 0.5339 0.000 0.656 0.288 0.056
#> TCGA-06-0147-01A-01 2 0.0188 0.7766 0.000 0.996 0.004 0.000
#> TCGA-06-0149-01A-05 2 0.7338 0.1605 0.000 0.464 0.376 0.160
#> TCGA-06-0152-01A-02 3 0.4359 0.6707 0.008 0.176 0.796 0.020
#> TCGA-06-0154-01A-02 2 0.3108 0.7487 0.000 0.872 0.112 0.016
#> TCGA-06-0164-01A-01 2 0.1059 0.7790 0.000 0.972 0.016 0.012
#> TCGA-06-0175-01A-01 2 0.6056 0.5424 0.000 0.660 0.248 0.092
#> TCGA-06-0176-01A-03 2 0.0779 0.7724 0.000 0.980 0.004 0.016
#> TCGA-06-0184-01A-01 2 0.6562 0.0942 0.000 0.552 0.088 0.360
#> TCGA-06-0189-01A-05 2 0.0804 0.7803 0.000 0.980 0.008 0.012
#> TCGA-06-0190-01A-01 2 0.2522 0.7662 0.000 0.908 0.076 0.016
#> TCGA-06-0194-01A-01 2 0.3557 0.7422 0.000 0.856 0.108 0.036
#> TCGA-06-0197-01A-02 2 0.0336 0.7785 0.000 0.992 0.008 0.000
#> TCGA-06-0210-01A-01 2 0.5446 0.5564 0.000 0.680 0.276 0.044
#> TCGA-06-0397-01A-01 2 0.2489 0.7695 0.000 0.912 0.068 0.020
#> TCGA-06-0409-01A-02 2 0.1059 0.7797 0.000 0.972 0.016 0.012
#> TCGA-06-0412-01A-01 2 0.5446 0.5564 0.000 0.680 0.276 0.044
#> TCGA-06-0644-01A-02 2 0.0927 0.7738 0.000 0.976 0.008 0.016
#> TCGA-06-0645-01A-01 2 0.3754 0.7366 0.000 0.852 0.084 0.064
#> TCGA-08-0346-01A-01 2 0.3787 0.7308 0.000 0.840 0.124 0.036
#> TCGA-08-0352-01A-01 2 0.6980 0.2027 0.000 0.484 0.400 0.116
#> TCGA-08-0360-01A-01 2 0.1833 0.7787 0.000 0.944 0.032 0.024
#> TCGA-08-0390-01A-01 2 0.5903 0.2685 0.000 0.616 0.052 0.332
#> TCGA-08-0392-01A-01 2 0.0927 0.7738 0.000 0.976 0.008 0.016
#> TCGA-08-0509-01A-01 2 0.5284 0.4471 0.000 0.696 0.040 0.264
#> TCGA-08-0510-01A-01 2 0.5267 0.6020 0.000 0.712 0.240 0.048
#> TCGA-08-0512-01A-01 2 0.1211 0.7823 0.000 0.960 0.040 0.000
#> TCGA-08-0522-01A-01 2 0.0927 0.7738 0.000 0.976 0.008 0.016
#> TCGA-12-0619-01A-01 2 0.0927 0.7802 0.000 0.976 0.008 0.016
#> TCGA-12-0620-01A-01 2 0.6206 0.3402 0.000 0.540 0.404 0.056
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.5910 0.5984 0.652 0.000 0.220 0.036 0.092
#> TCGA-02-0010-01A-01 1 0.0000 0.6800 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.6575 0.5000 0.544 0.000 0.144 0.024 0.288
#> TCGA-02-0014-01A-01 1 0.0000 0.6800 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.6800 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.5318 0.6562 0.708 0.000 0.124 0.016 0.152
#> TCGA-02-0028-01A-01 1 0.0000 0.6800 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.5910 0.5984 0.652 0.000 0.220 0.036 0.092
#> TCGA-02-0047-01A-01 4 0.7117 0.4762 0.084 0.076 0.148 0.632 0.060
#> TCGA-02-0048-01A-01 1 0.6022 0.4155 0.552 0.000 0.360 0.052 0.036
#> TCGA-02-0060-01A-01 5 0.8906 0.0213 0.248 0.012 0.248 0.228 0.264
#> TCGA-02-0069-01A-01 1 0.0000 0.6800 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.6012 0.6048 0.644 0.000 0.212 0.032 0.112
#> TCGA-02-0080-01A-01 1 0.5334 0.5082 0.612 0.000 0.052 0.008 0.328
#> TCGA-02-0084-01A-03 5 0.8195 0.3877 0.168 0.000 0.228 0.192 0.412
#> TCGA-02-0087-01A-01 5 0.8195 0.3877 0.168 0.000 0.228 0.192 0.412
#> TCGA-02-0104-01A-01 1 0.0162 0.6785 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0114-01A-01 1 0.0000 0.6800 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.6800 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.7824 0.0579 0.228 0.000 0.472 0.136 0.164
#> TCGA-02-0325-01A-01 3 0.7824 0.0579 0.228 0.000 0.472 0.136 0.164
#> TCGA-02-0338-01A-01 1 0.0000 0.6800 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.6800 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.5334 0.5082 0.612 0.000 0.052 0.008 0.328
#> TCGA-02-0439-01A-01 4 0.8721 -0.1211 0.212 0.020 0.232 0.380 0.156
#> TCGA-02-0440-01A-01 1 0.6690 0.5445 0.592 0.004 0.240 0.056 0.108
#> TCGA-02-0446-01A-01 4 0.7542 0.4287 0.124 0.072 0.152 0.592 0.060
#> TCGA-06-0128-01A-01 1 0.5918 0.4696 0.600 0.000 0.044 0.048 0.308
#> TCGA-06-0129-01A-01 1 0.4758 0.5776 0.696 0.000 0.032 0.012 0.260
#> TCGA-06-0146-01A-01 1 0.6795 0.3841 0.524 0.000 0.112 0.048 0.316
#> TCGA-06-0156-01A-01 4 0.7309 0.4669 0.104 0.080 0.144 0.616 0.056
#> TCGA-06-0166-01A-01 4 0.8528 0.2196 0.212 0.068 0.180 0.464 0.076
#> TCGA-06-0174-01A-01 1 0.5910 0.5984 0.652 0.000 0.220 0.036 0.092
#> TCGA-06-0177-01A-01 1 0.7329 0.4914 0.512 0.000 0.228 0.068 0.192
#> TCGA-06-0238-01A-02 1 0.7596 0.4203 0.464 0.000 0.248 0.072 0.216
#> TCGA-06-0241-01A-02 1 0.4923 0.6353 0.720 0.000 0.212 0.024 0.044
#> TCGA-06-0410-01A-01 1 0.4923 0.6355 0.720 0.000 0.212 0.024 0.044
#> TCGA-06-0413-01A-01 1 0.0000 0.6800 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.5752 0.6150 0.664 0.000 0.212 0.028 0.096
#> TCGA-06-0646-01A-01 4 0.7269 0.4755 0.096 0.084 0.144 0.620 0.056
#> TCGA-06-0648-01A-01 1 0.5679 0.6405 0.676 0.000 0.136 0.020 0.168
#> TCGA-08-0245-01A-01 1 0.4356 0.6544 0.768 0.000 0.180 0.024 0.028
#> TCGA-08-0344-01A-01 1 0.2304 0.6675 0.908 0.000 0.020 0.004 0.068
#> TCGA-08-0347-01A-01 4 0.7542 0.4287 0.124 0.072 0.152 0.592 0.060
#> TCGA-08-0348-01A-01 1 0.8896 -0.0452 0.312 0.020 0.236 0.268 0.164
#> TCGA-08-0350-01A-01 1 0.7074 0.2920 0.472 0.000 0.136 0.048 0.344
#> TCGA-08-0353-01A-01 3 0.4407 0.4603 0.244 0.000 0.724 0.012 0.020
#> TCGA-08-0359-01A-01 4 0.7578 0.3091 0.128 0.032 0.160 0.576 0.104
#> TCGA-08-0385-01A-01 1 0.4613 0.6441 0.756 0.000 0.120 0.004 0.120
#> TCGA-08-0517-01A-01 1 0.3163 0.6852 0.864 0.000 0.092 0.012 0.032
#> TCGA-08-0524-01A-01 1 0.0000 0.6800 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.6390 0.5397 0.572 0.000 0.264 0.020 0.144
#> TCGA-12-0618-01A-01 1 0.5513 0.6461 0.688 0.000 0.132 0.016 0.164
#> TCGA-02-0089-01A-01 4 0.4297 0.5999 0.000 0.132 0.056 0.792 0.020
#> TCGA-02-0113-01A-01 3 0.6341 0.4042 0.000 0.028 0.576 0.284 0.112
#> TCGA-02-0115-01A-01 4 0.2867 0.5071 0.000 0.044 0.004 0.880 0.072
#> TCGA-02-0451-01A-01 4 0.5397 0.5980 0.000 0.144 0.080 0.724 0.052
#> TCGA-06-0132-01A-02 4 0.2708 0.5041 0.000 0.044 0.000 0.884 0.072
#> TCGA-06-0133-01A-02 4 0.6067 0.1490 0.000 0.012 0.156 0.612 0.220
#> TCGA-06-0138-01A-02 4 0.5031 0.5586 0.004 0.092 0.072 0.768 0.064
#> TCGA-06-0160-01A-01 5 0.3707 0.5138 0.000 0.000 0.000 0.284 0.716
#> TCGA-06-0162-01A-01 4 0.4054 0.2243 0.000 0.012 0.008 0.744 0.236
#> TCGA-06-0167-01A-01 5 0.3707 0.5138 0.000 0.000 0.000 0.284 0.716
#> TCGA-06-0171-01A-02 4 0.5696 0.4901 0.008 0.060 0.124 0.720 0.088
#> TCGA-06-0173-01A-01 4 0.4607 0.5978 0.000 0.184 0.044 0.752 0.020
#> TCGA-06-0179-01A-02 4 0.2708 0.5041 0.000 0.044 0.000 0.884 0.072
#> TCGA-06-0182-01A-01 3 0.6201 0.2817 0.000 0.016 0.536 0.348 0.100
#> TCGA-06-0185-01A-01 3 0.5446 0.5437 0.000 0.032 0.648 0.280 0.040
#> TCGA-06-0195-01B-01 4 0.6036 -0.2314 0.012 0.012 0.052 0.492 0.432
#> TCGA-06-0208-01B-01 4 0.6177 0.1437 0.000 0.012 0.176 0.600 0.212
#> TCGA-06-0214-01A-02 4 0.5822 0.5954 0.008 0.140 0.100 0.704 0.048
#> TCGA-06-0219-01A-01 4 0.5704 -0.0574 0.000 0.012 0.064 0.568 0.356
#> TCGA-06-0221-01A-01 4 0.7180 -0.3339 0.120 0.012 0.036 0.440 0.392
#> TCGA-06-0237-01A-02 4 0.6461 0.1991 0.000 0.028 0.172 0.592 0.208
#> TCGA-06-0240-01A-02 5 0.3707 0.5138 0.000 0.000 0.000 0.284 0.716
#> TCGA-08-0349-01A-01 4 0.5912 0.4720 0.008 0.048 0.184 0.684 0.076
#> TCGA-08-0380-01A-01 4 0.3224 0.5600 0.000 0.080 0.012 0.864 0.044
#> TCGA-08-0386-01A-01 3 0.6973 0.3639 0.036 0.012 0.560 0.248 0.144
#> TCGA-08-0520-01A-01 3 0.6934 0.3030 0.008 0.028 0.520 0.304 0.140
#> TCGA-02-0007-01A-01 3 0.6200 0.4870 0.048 0.000 0.648 0.168 0.136
#> TCGA-02-0009-01A-01 3 0.0404 0.7504 0.000 0.000 0.988 0.012 0.000
#> TCGA-02-0016-01A-01 3 0.2490 0.7373 0.004 0.000 0.896 0.080 0.020
#> TCGA-02-0021-01A-01 3 0.0566 0.7453 0.000 0.000 0.984 0.004 0.012
#> TCGA-02-0023-01B-01 3 0.5751 0.5611 0.000 0.128 0.672 0.176 0.024
#> TCGA-02-0027-01A-01 3 0.8611 -0.1362 0.140 0.024 0.412 0.232 0.192
#> TCGA-02-0038-01A-01 4 0.5108 0.5970 0.000 0.184 0.076 0.720 0.020
#> TCGA-02-0043-01A-01 3 0.0510 0.7446 0.000 0.000 0.984 0.000 0.016
#> TCGA-02-0070-01A-01 2 0.6827 0.2295 0.000 0.424 0.316 0.256 0.004
#> TCGA-02-0102-01A-01 3 0.1419 0.7531 0.000 0.012 0.956 0.016 0.016
#> TCGA-02-0260-01A-03 3 0.1741 0.7293 0.024 0.000 0.936 0.000 0.040
#> TCGA-02-0269-01B-01 3 0.1741 0.7293 0.024 0.000 0.936 0.000 0.040
#> TCGA-02-0285-01A-01 3 0.2171 0.7482 0.000 0.024 0.912 0.064 0.000
#> TCGA-02-0289-01A-01 3 0.0912 0.7490 0.000 0.000 0.972 0.012 0.016
#> TCGA-02-0290-01A-01 3 0.2249 0.7484 0.000 0.040 0.920 0.020 0.020
#> TCGA-02-0317-01A-01 3 0.2919 0.6984 0.024 0.000 0.868 0.004 0.104
#> TCGA-02-0333-01A-02 3 0.1741 0.7293 0.024 0.000 0.936 0.000 0.040
#> TCGA-02-0422-01A-01 3 0.3124 0.7367 0.012 0.028 0.872 0.084 0.004
#> TCGA-02-0430-01A-01 3 0.2171 0.7482 0.000 0.024 0.912 0.064 0.000
#> TCGA-06-0125-01A-01 3 0.0290 0.7493 0.000 0.000 0.992 0.008 0.000
#> TCGA-06-0126-01A-01 3 0.1074 0.7495 0.012 0.000 0.968 0.016 0.004
#> TCGA-06-0137-01A-03 3 0.1484 0.7507 0.000 0.000 0.944 0.048 0.008
#> TCGA-06-0145-01A-04 3 0.1646 0.7549 0.000 0.020 0.944 0.032 0.004
#> TCGA-06-0148-01A-01 3 0.2067 0.7518 0.000 0.032 0.928 0.012 0.028
#> TCGA-06-0187-01A-01 3 0.3893 0.6908 0.000 0.052 0.804 0.140 0.004
#> TCGA-06-0211-01B-01 3 0.2043 0.7480 0.012 0.004 0.928 0.048 0.008
#> TCGA-06-0402-01A-01 3 0.0960 0.7498 0.000 0.004 0.972 0.008 0.016
#> TCGA-08-0246-01A-01 3 0.5677 0.5040 0.000 0.156 0.656 0.180 0.008
#> TCGA-08-0354-01A-01 3 0.5214 0.5775 0.000 0.156 0.712 0.120 0.012
#> TCGA-08-0355-01A-01 3 0.5912 0.4919 0.000 0.160 0.644 0.180 0.016
#> TCGA-08-0357-01A-01 3 0.3124 0.7367 0.012 0.028 0.872 0.084 0.004
#> TCGA-08-0358-01A-01 3 0.2919 0.6984 0.024 0.000 0.868 0.004 0.104
#> TCGA-08-0375-01A-01 3 0.2304 0.7204 0.020 0.000 0.908 0.004 0.068
#> TCGA-08-0511-01A-01 3 0.4659 0.6449 0.000 0.084 0.744 0.168 0.004
#> TCGA-08-0514-01A-01 3 0.3701 0.7061 0.000 0.060 0.824 0.112 0.004
#> TCGA-08-0518-01A-01 3 0.0912 0.7539 0.000 0.016 0.972 0.012 0.000
#> TCGA-08-0529-01A-02 3 0.2171 0.7482 0.000 0.024 0.912 0.064 0.000
#> TCGA-08-0531-01A-01 3 0.0798 0.7537 0.000 0.008 0.976 0.016 0.000
#> TCGA-02-0057-01A-01 4 0.4729 0.5982 0.000 0.180 0.048 0.748 0.024
#> TCGA-02-0004-01A-01 2 0.0693 0.7534 0.000 0.980 0.000 0.012 0.008
#> TCGA-02-0006-01B-01 4 0.4709 0.5901 0.000 0.196 0.044 0.740 0.020
#> TCGA-02-0025-01A-01 2 0.2341 0.7319 0.000 0.912 0.012 0.020 0.056
#> TCGA-02-0033-01A-01 2 0.0963 0.7638 0.000 0.964 0.000 0.036 0.000
#> TCGA-02-0034-01A-01 2 0.2264 0.7639 0.000 0.912 0.024 0.060 0.004
#> TCGA-02-0039-01A-01 4 0.5753 -0.0432 0.000 0.440 0.064 0.488 0.008
#> TCGA-02-0051-01A-01 2 0.0963 0.7367 0.000 0.964 0.000 0.000 0.036
#> TCGA-02-0054-01A-01 4 0.4892 0.5824 0.000 0.208 0.044 0.724 0.024
#> TCGA-02-0055-01A-01 2 0.0693 0.7506 0.000 0.980 0.000 0.008 0.012
#> TCGA-02-0059-01A-01 2 0.0865 0.7612 0.000 0.972 0.000 0.024 0.004
#> TCGA-02-0064-01A-01 2 0.3622 0.7362 0.000 0.816 0.048 0.136 0.000
#> TCGA-02-0075-01A-01 2 0.4219 0.7093 0.000 0.772 0.072 0.156 0.000
#> TCGA-02-0079-01A-03 4 0.7261 0.4074 0.000 0.256 0.132 0.524 0.088
#> TCGA-02-0085-01A-01 4 0.4617 0.5874 0.000 0.196 0.044 0.744 0.016
#> TCGA-02-0086-01A-01 2 0.4818 0.6615 0.000 0.720 0.100 0.180 0.000
#> TCGA-02-0099-01A-01 4 0.4765 0.5763 0.000 0.212 0.040 0.728 0.020
#> TCGA-02-0106-01A-01 2 0.0854 0.7554 0.000 0.976 0.008 0.004 0.012
#> TCGA-02-0107-01A-01 2 0.1410 0.7630 0.000 0.940 0.000 0.060 0.000
#> TCGA-02-0111-01A-01 2 0.2074 0.7559 0.000 0.896 0.000 0.104 0.000
#> TCGA-02-0326-01A-01 3 0.7551 0.1586 0.004 0.048 0.444 0.296 0.208
#> TCGA-02-0337-01A-01 4 0.5194 0.5675 0.008 0.220 0.064 0.700 0.008
#> TCGA-06-0122-01A-01 2 0.6742 0.3102 0.000 0.460 0.264 0.272 0.004
#> TCGA-06-0124-01A-01 2 0.4504 0.6923 0.000 0.748 0.084 0.168 0.000
#> TCGA-06-0130-01A-01 2 0.0798 0.7486 0.000 0.976 0.000 0.008 0.016
#> TCGA-06-0139-01A-01 2 0.0963 0.7619 0.000 0.964 0.000 0.036 0.000
#> TCGA-06-0143-01A-01 2 0.6780 0.2844 0.000 0.448 0.268 0.280 0.004
#> TCGA-06-0147-01A-01 2 0.0963 0.7619 0.000 0.964 0.000 0.036 0.000
#> TCGA-06-0149-01A-05 4 0.7104 0.1342 0.000 0.280 0.332 0.376 0.012
#> TCGA-06-0152-01A-02 3 0.5629 0.6435 0.000 0.092 0.716 0.080 0.112
#> TCGA-06-0154-01A-02 2 0.4986 0.6700 0.000 0.716 0.104 0.176 0.004
#> TCGA-06-0164-01A-01 2 0.2011 0.7601 0.000 0.908 0.004 0.088 0.000
#> TCGA-06-0175-01A-01 2 0.6774 0.2882 0.000 0.468 0.224 0.300 0.008
#> TCGA-06-0176-01A-03 2 0.0693 0.7518 0.000 0.980 0.000 0.008 0.012
#> TCGA-06-0184-01A-01 4 0.5570 0.3034 0.000 0.332 0.060 0.596 0.012
#> TCGA-06-0189-01A-05 2 0.1124 0.7647 0.000 0.960 0.000 0.036 0.004
#> TCGA-06-0190-01A-01 2 0.4393 0.6982 0.000 0.756 0.076 0.168 0.000
#> TCGA-06-0194-01A-01 2 0.5010 0.6336 0.000 0.688 0.088 0.224 0.000
#> TCGA-06-0197-01A-02 2 0.0963 0.7638 0.000 0.964 0.000 0.036 0.000
#> TCGA-06-0210-01A-01 2 0.6713 0.3214 0.000 0.468 0.256 0.272 0.004
#> TCGA-06-0397-01A-01 2 0.3115 0.7393 0.000 0.876 0.056 0.048 0.020
#> TCGA-06-0409-01A-02 2 0.2707 0.7490 0.000 0.860 0.008 0.132 0.000
#> TCGA-06-0412-01A-01 2 0.6713 0.3214 0.000 0.468 0.256 0.272 0.004
#> TCGA-06-0644-01A-02 2 0.0404 0.7492 0.000 0.988 0.000 0.000 0.012
#> TCGA-06-0645-01A-01 2 0.5010 0.6303 0.000 0.676 0.076 0.248 0.000
#> TCGA-08-0346-01A-01 2 0.5205 0.6178 0.000 0.672 0.104 0.224 0.000
#> TCGA-08-0352-01A-01 3 0.6932 -0.1166 0.000 0.300 0.376 0.320 0.004
#> TCGA-08-0360-01A-01 2 0.3060 0.7477 0.000 0.848 0.024 0.128 0.000
#> TCGA-08-0390-01A-01 4 0.4973 0.1380 0.000 0.408 0.024 0.564 0.004
#> TCGA-08-0392-01A-01 2 0.0963 0.7367 0.000 0.964 0.000 0.000 0.036
#> TCGA-08-0509-01A-01 2 0.4637 0.2160 0.000 0.536 0.012 0.452 0.000
#> TCGA-08-0510-01A-01 2 0.6562 0.3700 0.000 0.500 0.216 0.280 0.004
#> TCGA-08-0512-01A-01 2 0.3106 0.7418 0.000 0.844 0.024 0.132 0.000
#> TCGA-08-0522-01A-01 2 0.0703 0.7432 0.000 0.976 0.000 0.000 0.024
#> TCGA-12-0619-01A-01 2 0.1282 0.7660 0.000 0.952 0.000 0.044 0.004
#> TCGA-12-0620-01A-01 2 0.6952 0.1567 0.000 0.392 0.380 0.216 0.012
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.6335 0.37647 0.564 0.000 0.172 0.020 0.216 0.028
#> TCGA-02-0010-01A-01 1 0.0000 0.57328 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.6520 -0.23896 0.420 0.000 0.104 0.044 0.416 0.016
#> TCGA-02-0014-01A-01 1 0.0000 0.57328 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0458 0.57261 0.984 0.000 0.000 0.000 0.016 0.000
#> TCGA-02-0026-01B-01 1 0.5283 0.37336 0.632 0.000 0.092 0.016 0.256 0.004
#> TCGA-02-0028-01A-01 1 0.0000 0.57328 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.6335 0.37647 0.564 0.000 0.172 0.020 0.216 0.028
#> TCGA-02-0047-01A-01 6 0.5937 0.51553 0.028 0.044 0.104 0.008 0.148 0.668
#> TCGA-02-0048-01A-01 1 0.6424 0.17017 0.496 0.000 0.316 0.004 0.136 0.048
#> TCGA-02-0060-01A-01 5 0.8567 0.29102 0.160 0.000 0.180 0.104 0.340 0.216
#> TCGA-02-0069-01A-01 1 0.0146 0.57348 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0074-01A-01 1 0.6275 0.35563 0.552 0.000 0.164 0.016 0.244 0.024
#> TCGA-02-0080-01A-01 5 0.5134 0.20519 0.468 0.000 0.028 0.032 0.472 0.000
#> TCGA-02-0084-01A-03 5 0.6011 0.25988 0.020 0.000 0.136 0.060 0.644 0.140
#> TCGA-02-0087-01A-01 5 0.6011 0.25988 0.020 0.000 0.136 0.060 0.644 0.140
#> TCGA-02-0104-01A-01 1 0.0146 0.57075 0.996 0.000 0.000 0.004 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0260 0.57248 0.992 0.000 0.000 0.000 0.008 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.57328 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.7491 -0.14618 0.156 0.000 0.416 0.020 0.292 0.116
#> TCGA-02-0325-01A-01 3 0.7491 -0.14618 0.156 0.000 0.416 0.020 0.292 0.116
#> TCGA-02-0338-01A-01 1 0.0000 0.57328 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.57328 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 5 0.5134 0.20519 0.468 0.000 0.028 0.032 0.472 0.000
#> TCGA-02-0439-01A-01 6 0.7755 -0.14778 0.132 0.000 0.172 0.028 0.268 0.400
#> TCGA-02-0440-01A-01 1 0.6852 0.24069 0.492 0.000 0.180 0.016 0.260 0.052
#> TCGA-02-0446-01A-01 6 0.6474 0.48363 0.064 0.044 0.108 0.004 0.156 0.624
#> TCGA-06-0128-01A-01 5 0.5658 0.20556 0.452 0.000 0.020 0.032 0.464 0.032
#> TCGA-06-0129-01A-01 1 0.4496 -0.05395 0.552 0.000 0.008 0.012 0.424 0.004
#> TCGA-06-0146-01A-01 5 0.6327 0.35035 0.376 0.000 0.088 0.024 0.480 0.032
#> TCGA-06-0156-01A-01 6 0.6143 0.51129 0.044 0.048 0.100 0.004 0.152 0.652
#> TCGA-06-0166-01A-01 6 0.7813 0.25485 0.152 0.044 0.128 0.012 0.180 0.484
#> TCGA-06-0174-01A-01 1 0.6335 0.37647 0.564 0.000 0.172 0.020 0.216 0.028
#> TCGA-06-0177-01A-01 1 0.7176 0.00713 0.404 0.000 0.176 0.020 0.340 0.060
#> TCGA-06-0238-01A-02 5 0.7330 -0.00336 0.356 0.000 0.196 0.024 0.364 0.060
#> TCGA-06-0241-01A-02 1 0.5574 0.44554 0.640 0.000 0.164 0.008 0.168 0.020
#> TCGA-06-0410-01A-01 1 0.5469 0.44413 0.644 0.000 0.168 0.004 0.164 0.020
#> TCGA-06-0413-01A-01 1 0.0458 0.57261 0.984 0.000 0.000 0.000 0.016 0.000
#> TCGA-06-0414-01A-01 1 0.6097 0.38779 0.576 0.000 0.160 0.016 0.228 0.020
#> TCGA-06-0646-01A-01 6 0.6134 0.51638 0.044 0.052 0.100 0.004 0.144 0.656
#> TCGA-06-0648-01A-01 1 0.5691 0.31846 0.584 0.000 0.100 0.020 0.288 0.008
#> TCGA-08-0245-01A-01 1 0.4922 0.48491 0.704 0.000 0.136 0.004 0.140 0.016
#> TCGA-08-0344-01A-01 1 0.2473 0.48902 0.876 0.000 0.012 0.008 0.104 0.000
#> TCGA-08-0347-01A-01 6 0.6474 0.48363 0.064 0.044 0.108 0.004 0.156 0.624
#> TCGA-08-0348-01A-01 5 0.8061 0.23277 0.216 0.000 0.176 0.024 0.308 0.276
#> TCGA-08-0350-01A-01 5 0.6570 0.39779 0.324 0.000 0.112 0.032 0.500 0.032
#> TCGA-08-0353-01A-01 3 0.4448 0.41328 0.216 0.000 0.708 0.000 0.068 0.008
#> TCGA-08-0359-01A-01 6 0.6378 0.37446 0.060 0.008 0.108 0.016 0.204 0.604
#> TCGA-08-0385-01A-01 1 0.4690 0.32635 0.704 0.000 0.108 0.004 0.180 0.004
#> TCGA-08-0517-01A-01 1 0.3146 0.54525 0.848 0.000 0.060 0.000 0.080 0.012
#> TCGA-08-0524-01A-01 1 0.0000 0.57328 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.6370 0.16606 0.484 0.000 0.212 0.008 0.280 0.016
#> TCGA-12-0618-01A-01 1 0.5539 0.33305 0.600 0.000 0.100 0.020 0.276 0.004
#> TCGA-02-0089-01A-01 6 0.3601 0.59350 0.000 0.084 0.036 0.024 0.020 0.836
#> TCGA-02-0113-01A-01 3 0.6690 0.34622 0.000 0.008 0.504 0.052 0.192 0.244
#> TCGA-02-0115-01A-01 6 0.2611 0.47172 0.000 0.012 0.000 0.116 0.008 0.864
#> TCGA-02-0451-01A-01 6 0.4811 0.58995 0.000 0.092 0.048 0.044 0.052 0.764
#> TCGA-06-0132-01A-02 6 0.2755 0.46561 0.000 0.012 0.000 0.120 0.012 0.856
#> TCGA-06-0133-01A-02 6 0.6989 -0.16138 0.000 0.008 0.088 0.172 0.248 0.484
#> TCGA-06-0138-01A-02 6 0.4576 0.53401 0.000 0.060 0.044 0.056 0.056 0.784
#> TCGA-06-0160-01A-01 4 0.2843 0.74182 0.000 0.000 0.000 0.848 0.036 0.116
#> TCGA-06-0162-01A-01 6 0.5507 -0.11321 0.000 0.008 0.000 0.216 0.180 0.596
#> TCGA-06-0167-01A-01 4 0.2843 0.74182 0.000 0.000 0.000 0.848 0.036 0.116
#> TCGA-06-0171-01A-02 6 0.5538 0.44859 0.000 0.036 0.076 0.080 0.100 0.708
#> TCGA-06-0173-01A-01 6 0.3727 0.60007 0.000 0.132 0.024 0.008 0.028 0.808
#> TCGA-06-0179-01A-02 6 0.2755 0.46561 0.000 0.012 0.000 0.120 0.012 0.856
#> TCGA-06-0182-01A-01 3 0.6623 0.29655 0.000 0.008 0.516 0.076 0.120 0.280
#> TCGA-06-0185-01A-01 3 0.5439 0.54274 0.000 0.016 0.632 0.036 0.048 0.268
#> TCGA-06-0195-01B-01 4 0.6879 0.50426 0.012 0.008 0.024 0.416 0.196 0.344
#> TCGA-06-0208-01B-01 6 0.7134 -0.15962 0.000 0.008 0.108 0.164 0.252 0.468
#> TCGA-06-0214-01A-02 6 0.5056 0.58991 0.000 0.088 0.064 0.044 0.056 0.748
#> TCGA-06-0219-01A-01 6 0.6775 -0.45127 0.000 0.008 0.036 0.336 0.204 0.416
#> TCGA-06-0221-01A-01 4 0.7233 0.52276 0.028 0.008 0.016 0.336 0.304 0.308
#> TCGA-06-0237-01A-02 6 0.7171 -0.08499 0.000 0.016 0.100 0.164 0.236 0.484
#> TCGA-06-0240-01A-02 4 0.2843 0.74182 0.000 0.000 0.000 0.848 0.036 0.116
#> TCGA-08-0349-01A-01 6 0.5851 0.44712 0.000 0.020 0.136 0.056 0.128 0.660
#> TCGA-08-0380-01A-01 6 0.2839 0.53832 0.000 0.040 0.000 0.052 0.032 0.876
#> TCGA-08-0386-01A-01 3 0.7205 0.30498 0.032 0.000 0.472 0.056 0.236 0.204
#> TCGA-08-0520-01A-01 3 0.7125 0.21943 0.004 0.008 0.432 0.056 0.232 0.268
#> TCGA-02-0007-01A-01 3 0.6583 0.40730 0.040 0.000 0.572 0.052 0.228 0.108
#> TCGA-02-0009-01A-01 3 0.0458 0.74372 0.000 0.000 0.984 0.000 0.000 0.016
#> TCGA-02-0016-01A-01 3 0.2601 0.73403 0.004 0.000 0.888 0.016 0.024 0.068
#> TCGA-02-0021-01A-01 3 0.0405 0.73875 0.000 0.000 0.988 0.000 0.008 0.004
#> TCGA-02-0023-01B-01 3 0.5492 0.54345 0.000 0.096 0.656 0.008 0.036 0.204
#> TCGA-02-0027-01A-01 3 0.8261 -0.20397 0.068 0.008 0.352 0.080 0.260 0.232
#> TCGA-02-0038-01A-01 6 0.4227 0.59927 0.000 0.132 0.052 0.012 0.024 0.780
#> TCGA-02-0043-01A-01 3 0.0458 0.73893 0.000 0.000 0.984 0.000 0.016 0.000
#> TCGA-02-0070-01A-01 2 0.6439 0.16523 0.000 0.372 0.300 0.004 0.008 0.316
#> TCGA-02-0102-01A-01 3 0.1317 0.74631 0.000 0.008 0.956 0.004 0.016 0.016
#> TCGA-02-0260-01A-03 3 0.1829 0.71647 0.012 0.000 0.920 0.004 0.064 0.000
#> TCGA-02-0269-01B-01 3 0.1829 0.71647 0.012 0.000 0.920 0.004 0.064 0.000
#> TCGA-02-0285-01A-01 3 0.2002 0.74397 0.000 0.012 0.908 0.004 0.000 0.076
#> TCGA-02-0289-01A-01 3 0.1088 0.74260 0.000 0.000 0.960 0.000 0.024 0.016
#> TCGA-02-0290-01A-01 3 0.2176 0.74194 0.000 0.036 0.916 0.004 0.024 0.020
#> TCGA-02-0317-01A-01 3 0.3058 0.67627 0.012 0.000 0.840 0.024 0.124 0.000
#> TCGA-02-0333-01A-02 3 0.1769 0.71854 0.012 0.000 0.924 0.004 0.060 0.000
#> TCGA-02-0422-01A-01 3 0.2866 0.73215 0.000 0.024 0.864 0.000 0.020 0.092
#> TCGA-02-0430-01A-01 3 0.2002 0.74397 0.000 0.012 0.908 0.004 0.000 0.076
#> TCGA-06-0125-01A-01 3 0.0363 0.74243 0.000 0.000 0.988 0.000 0.000 0.012
#> TCGA-06-0126-01A-01 3 0.1092 0.74286 0.000 0.000 0.960 0.000 0.020 0.020
#> TCGA-06-0137-01A-03 3 0.1511 0.74561 0.000 0.000 0.940 0.004 0.012 0.044
#> TCGA-06-0145-01A-04 3 0.1624 0.74834 0.000 0.012 0.936 0.000 0.008 0.044
#> TCGA-06-0148-01A-01 3 0.2074 0.74449 0.000 0.028 0.920 0.004 0.036 0.012
#> TCGA-06-0187-01A-01 3 0.3913 0.67587 0.000 0.040 0.784 0.008 0.012 0.156
#> TCGA-06-0211-01B-01 3 0.1909 0.74284 0.000 0.000 0.920 0.004 0.024 0.052
#> TCGA-06-0402-01A-01 3 0.0820 0.74331 0.000 0.000 0.972 0.000 0.016 0.012
#> TCGA-08-0246-01A-01 3 0.5375 0.48141 0.000 0.116 0.636 0.004 0.016 0.228
#> TCGA-08-0354-01A-01 3 0.4991 0.56844 0.000 0.120 0.700 0.004 0.020 0.156
#> TCGA-08-0355-01A-01 3 0.5580 0.46737 0.000 0.124 0.624 0.004 0.024 0.224
#> TCGA-08-0357-01A-01 3 0.2866 0.73215 0.000 0.024 0.864 0.000 0.020 0.092
#> TCGA-08-0358-01A-01 3 0.3058 0.67627 0.012 0.000 0.840 0.024 0.124 0.000
#> TCGA-08-0375-01A-01 3 0.2376 0.70321 0.008 0.000 0.884 0.012 0.096 0.000
#> TCGA-08-0511-01A-01 3 0.4417 0.62172 0.000 0.068 0.728 0.004 0.008 0.192
#> TCGA-08-0514-01A-01 3 0.3646 0.69253 0.000 0.048 0.804 0.004 0.008 0.136
#> TCGA-08-0518-01A-01 3 0.1109 0.74718 0.000 0.012 0.964 0.004 0.004 0.016
#> TCGA-08-0529-01A-02 3 0.2002 0.74397 0.000 0.012 0.908 0.004 0.000 0.076
#> TCGA-08-0531-01A-01 3 0.0806 0.74709 0.000 0.008 0.972 0.000 0.000 0.020
#> TCGA-02-0057-01A-01 6 0.3704 0.59838 0.000 0.128 0.028 0.012 0.020 0.812
#> TCGA-02-0004-01A-01 2 0.0914 0.73322 0.000 0.968 0.000 0.016 0.000 0.016
#> TCGA-02-0006-01B-01 6 0.3688 0.59777 0.000 0.144 0.024 0.008 0.020 0.804
#> TCGA-02-0025-01A-01 2 0.3121 0.68335 0.000 0.864 0.008 0.064 0.040 0.024
#> TCGA-02-0033-01A-01 2 0.1265 0.74536 0.000 0.948 0.000 0.008 0.000 0.044
#> TCGA-02-0034-01A-01 2 0.2588 0.74118 0.000 0.876 0.024 0.008 0.000 0.092
#> TCGA-02-0039-01A-01 6 0.5190 0.04297 0.000 0.396 0.040 0.000 0.028 0.536
#> TCGA-02-0051-01A-01 2 0.2265 0.68703 0.000 0.896 0.000 0.052 0.052 0.000
#> TCGA-02-0054-01A-01 6 0.3956 0.59635 0.000 0.156 0.028 0.008 0.024 0.784
#> TCGA-02-0055-01A-01 2 0.0717 0.73040 0.000 0.976 0.000 0.016 0.000 0.008
#> TCGA-02-0059-01A-01 2 0.1296 0.74158 0.000 0.952 0.000 0.012 0.004 0.032
#> TCGA-02-0064-01A-01 2 0.3758 0.70406 0.000 0.772 0.048 0.004 0.000 0.176
#> TCGA-02-0075-01A-01 2 0.4253 0.67407 0.000 0.728 0.072 0.004 0.000 0.196
#> TCGA-02-0079-01A-03 6 0.7329 0.40941 0.000 0.200 0.084 0.064 0.132 0.520
#> TCGA-02-0085-01A-01 6 0.3978 0.58828 0.000 0.156 0.024 0.012 0.024 0.784
#> TCGA-02-0086-01A-01 2 0.4632 0.63052 0.000 0.688 0.092 0.004 0.000 0.216
#> TCGA-02-0099-01A-01 6 0.3836 0.59323 0.000 0.160 0.024 0.008 0.020 0.788
#> TCGA-02-0106-01A-01 2 0.1425 0.73223 0.000 0.952 0.008 0.020 0.012 0.008
#> TCGA-02-0107-01A-01 2 0.1700 0.74373 0.000 0.916 0.000 0.004 0.000 0.080
#> TCGA-02-0111-01A-01 2 0.2234 0.73681 0.000 0.872 0.000 0.004 0.000 0.124
#> TCGA-02-0326-01A-01 3 0.7590 0.08086 0.004 0.000 0.360 0.148 0.228 0.260
#> TCGA-02-0337-01A-01 6 0.4372 0.58743 0.000 0.176 0.040 0.000 0.040 0.744
#> TCGA-06-0122-01A-01 2 0.6353 0.24032 0.000 0.408 0.248 0.004 0.008 0.332
#> TCGA-06-0124-01A-01 2 0.4465 0.65548 0.000 0.704 0.080 0.004 0.000 0.212
#> TCGA-06-0130-01A-01 2 0.0862 0.72855 0.000 0.972 0.000 0.016 0.004 0.008
#> TCGA-06-0139-01A-01 2 0.1152 0.74332 0.000 0.952 0.000 0.004 0.000 0.044
#> TCGA-06-0143-01A-01 2 0.6372 0.21293 0.000 0.396 0.252 0.004 0.008 0.340
#> TCGA-06-0147-01A-01 2 0.1152 0.74332 0.000 0.952 0.000 0.004 0.000 0.044
#> TCGA-06-0149-01A-05 6 0.6644 0.18757 0.000 0.240 0.304 0.004 0.028 0.424
#> TCGA-06-0152-01A-02 3 0.5992 0.60716 0.000 0.048 0.664 0.060 0.144 0.084
#> TCGA-06-0154-01A-02 2 0.4906 0.62749 0.000 0.668 0.100 0.004 0.004 0.224
#> TCGA-06-0164-01A-01 2 0.2196 0.74072 0.000 0.884 0.004 0.004 0.000 0.108
#> TCGA-06-0175-01A-01 2 0.6260 0.21354 0.000 0.420 0.212 0.008 0.004 0.356
#> TCGA-06-0176-01A-03 2 0.1053 0.73014 0.000 0.964 0.000 0.020 0.004 0.012
#> TCGA-06-0184-01A-01 6 0.4691 0.35547 0.000 0.284 0.048 0.008 0.004 0.656
#> TCGA-06-0189-01A-05 2 0.1511 0.74558 0.000 0.940 0.000 0.012 0.004 0.044
#> TCGA-06-0190-01A-01 2 0.4366 0.66190 0.000 0.712 0.072 0.004 0.000 0.212
#> TCGA-06-0194-01A-01 2 0.4770 0.59791 0.000 0.652 0.080 0.004 0.000 0.264
#> TCGA-06-0197-01A-02 2 0.1265 0.74536 0.000 0.948 0.000 0.008 0.000 0.044
#> TCGA-06-0210-01A-01 2 0.6330 0.25205 0.000 0.416 0.240 0.004 0.008 0.332
#> TCGA-06-0397-01A-01 2 0.3464 0.71256 0.000 0.848 0.048 0.028 0.016 0.060
#> TCGA-06-0409-01A-02 2 0.2773 0.72906 0.000 0.836 0.008 0.004 0.000 0.152
#> TCGA-06-0412-01A-01 2 0.6330 0.25205 0.000 0.416 0.240 0.004 0.008 0.332
#> TCGA-06-0644-01A-02 2 0.1138 0.72374 0.000 0.960 0.000 0.024 0.012 0.004
#> TCGA-06-0645-01A-01 2 0.4892 0.59199 0.000 0.632 0.072 0.008 0.000 0.288
#> TCGA-08-0346-01A-01 2 0.4967 0.57598 0.000 0.632 0.096 0.004 0.000 0.268
#> TCGA-08-0352-01A-01 6 0.6399 0.09051 0.000 0.260 0.360 0.004 0.008 0.368
#> TCGA-08-0360-01A-01 2 0.3349 0.71867 0.000 0.804 0.024 0.008 0.000 0.164
#> TCGA-08-0390-01A-01 6 0.4472 0.19339 0.000 0.372 0.016 0.008 0.004 0.600
#> TCGA-08-0392-01A-01 2 0.2265 0.68703 0.000 0.896 0.000 0.052 0.052 0.000
#> TCGA-08-0509-01A-01 2 0.4096 0.17474 0.000 0.508 0.008 0.000 0.000 0.484
#> TCGA-08-0510-01A-01 2 0.6111 0.29712 0.000 0.448 0.204 0.004 0.004 0.340
#> TCGA-08-0512-01A-01 2 0.3419 0.71364 0.000 0.796 0.024 0.008 0.000 0.172
#> TCGA-08-0522-01A-01 2 0.1334 0.71479 0.000 0.948 0.000 0.032 0.020 0.000
#> TCGA-12-0619-01A-01 2 0.1644 0.74727 0.000 0.932 0.000 0.012 0.004 0.052
#> TCGA-12-0620-01A-01 3 0.6558 -0.18408 0.000 0.348 0.368 0.004 0.016 0.264
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> SD:hclust 110 5.73e-23 2
#> SD:hclust 84 1.19e-33 3
#> SD:hclust 132 1.20e-64 4
#> SD:hclust 120 3.81e-55 5
#> SD:hclust 102 2.12e-42 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "kmeans"]
# you can also extract it by
# res = res_list["SD:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.777 0.895 0.954 0.4928 0.502 0.502
#> 3 3 0.842 0.898 0.955 0.3386 0.669 0.436
#> 4 4 0.907 0.917 0.963 0.1379 0.844 0.583
#> 5 5 0.766 0.686 0.819 0.0490 0.978 0.914
#> 6 6 0.723 0.620 0.756 0.0357 0.932 0.722
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.9209 0.5162 0.664 0.336
#> TCGA-02-0048-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0084-01A-03 1 0.6148 0.8359 0.848 0.152
#> TCGA-02-0087-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0104-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.4298 0.8972 0.912 0.088
#> TCGA-02-0325-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.9954 0.1517 0.540 0.460
#> TCGA-06-0128-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.5737 0.8518 0.864 0.136
#> TCGA-06-0166-01A-01 1 0.8813 0.5993 0.700 0.300
#> TCGA-06-0174-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.5408 0.8463 0.124 0.876
#> TCGA-06-0648-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.4690 0.8860 0.900 0.100
#> TCGA-08-0348-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-08-0353-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.1633 0.9365 0.024 0.976
#> TCGA-02-0115-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.6247 0.8086 0.156 0.844
#> TCGA-06-0138-01A-02 2 0.5059 0.8586 0.112 0.888
#> TCGA-06-0160-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0171-01A-02 2 0.9996 0.0227 0.488 0.512
#> TCGA-06-0173-01A-01 2 0.4298 0.8819 0.088 0.912
#> TCGA-06-0179-01A-02 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.4939 0.8626 0.108 0.892
#> TCGA-06-0185-01A-01 2 0.7950 0.6866 0.240 0.760
#> TCGA-06-0195-01B-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.7219 0.7493 0.200 0.800
#> TCGA-06-0214-01A-02 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.9850 0.2408 0.428 0.572
#> TCGA-06-0221-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-06-0237-01A-02 1 0.4939 0.8803 0.892 0.108
#> TCGA-06-0240-01A-02 1 0.0376 0.9430 0.996 0.004
#> TCGA-08-0349-01A-01 1 0.9460 0.4628 0.636 0.364
#> TCGA-08-0380-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.4161 0.8997 0.916 0.084
#> TCGA-08-0520-01A-01 2 0.5519 0.8426 0.128 0.872
#> TCGA-02-0007-01A-01 1 0.4298 0.8972 0.912 0.088
#> TCGA-02-0009-01A-01 1 0.5842 0.8480 0.860 0.140
#> TCGA-02-0016-01A-01 1 0.4298 0.8972 0.912 0.088
#> TCGA-02-0021-01A-01 2 0.9608 0.3737 0.384 0.616
#> TCGA-02-0023-01B-01 2 0.2043 0.9301 0.032 0.968
#> TCGA-02-0027-01A-01 1 0.6712 0.8051 0.824 0.176
#> TCGA-02-0038-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0043-01A-01 1 0.8144 0.6923 0.748 0.252
#> TCGA-02-0070-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0102-01A-01 2 0.9866 0.2285 0.432 0.568
#> TCGA-02-0260-01A-03 1 0.0000 0.9449 1.000 0.000
#> TCGA-02-0269-01B-01 1 0.1843 0.9321 0.972 0.028
#> TCGA-02-0285-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0289-01A-01 1 0.4562 0.8911 0.904 0.096
#> TCGA-02-0290-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0317-01A-01 1 0.4431 0.8943 0.908 0.092
#> TCGA-02-0333-01A-02 1 0.4431 0.8943 0.908 0.092
#> TCGA-02-0422-01A-01 2 0.5629 0.8374 0.132 0.868
#> TCGA-02-0430-01A-01 2 0.9954 0.1285 0.460 0.540
#> TCGA-06-0125-01A-01 1 0.5059 0.8769 0.888 0.112
#> TCGA-06-0126-01A-01 1 0.2043 0.9302 0.968 0.032
#> TCGA-06-0137-01A-03 1 0.4298 0.8972 0.912 0.088
#> TCGA-06-0145-01A-04 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0148-01A-01 2 0.0672 0.9479 0.008 0.992
#> TCGA-06-0187-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0211-01B-01 1 0.4161 0.8999 0.916 0.084
#> TCGA-06-0402-01A-01 2 0.6887 0.7733 0.184 0.816
#> TCGA-08-0246-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0357-01A-01 1 0.9491 0.4547 0.632 0.368
#> TCGA-08-0358-01A-01 1 0.0000 0.9449 1.000 0.000
#> TCGA-08-0375-01A-01 1 0.1843 0.9321 0.972 0.028
#> TCGA-08-0511-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0514-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.3114 0.9110 0.056 0.944
#> TCGA-08-0529-01A-02 2 0.5059 0.8590 0.112 0.888
#> TCGA-08-0531-01A-01 2 0.6048 0.8191 0.148 0.852
#> TCGA-02-0057-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-02-0326-01A-01 1 0.4431 0.8943 0.908 0.092
#> TCGA-02-0337-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9536 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9536 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.9536 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 3 0.6062 0.3943 0.384 0.000 0.616
#> TCGA-02-0048-01A-01 3 0.6280 0.1522 0.460 0.000 0.540
#> TCGA-02-0060-01A-01 1 0.3941 0.8256 0.844 0.000 0.156
#> TCGA-02-0069-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0084-01A-03 3 0.6473 0.5347 0.312 0.020 0.668
#> TCGA-02-0087-01A-01 1 0.3879 0.8292 0.848 0.000 0.152
#> TCGA-02-0104-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.1031 0.9153 0.024 0.000 0.976
#> TCGA-02-0325-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0439-01A-01 3 0.5733 0.5268 0.324 0.000 0.676
#> TCGA-02-0440-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.5958 0.5758 0.692 0.008 0.300
#> TCGA-06-0128-01A-01 1 0.0237 0.9598 0.996 0.000 0.004
#> TCGA-06-0129-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 3 0.6033 0.5061 0.336 0.004 0.660
#> TCGA-06-0166-01A-01 3 0.5982 0.5228 0.328 0.004 0.668
#> TCGA-06-0174-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.0592 0.9227 0.000 0.012 0.988
#> TCGA-06-0648-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-08-0347-01A-01 3 0.5178 0.6502 0.256 0.000 0.744
#> TCGA-08-0348-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-08-0353-01A-01 3 0.0237 0.9271 0.004 0.000 0.996
#> TCGA-08-0359-01A-01 1 0.4235 0.8007 0.824 0.000 0.176
#> TCGA-08-0385-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.9628 1.000 0.000 0.000
#> TCGA-02-0089-01A-01 3 0.4452 0.7558 0.000 0.192 0.808
#> TCGA-02-0113-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0115-01A-01 3 0.3879 0.8023 0.000 0.152 0.848
#> TCGA-02-0451-01A-01 3 0.4235 0.7751 0.000 0.176 0.824
#> TCGA-06-0132-01A-02 2 0.5254 0.6326 0.000 0.736 0.264
#> TCGA-06-0133-01A-02 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 3 0.0592 0.9227 0.000 0.012 0.988
#> TCGA-06-0160-01A-01 1 0.4121 0.8115 0.832 0.000 0.168
#> TCGA-06-0162-01A-01 3 0.3816 0.8065 0.000 0.148 0.852
#> TCGA-06-0167-01A-01 1 0.4121 0.8115 0.832 0.000 0.168
#> TCGA-06-0171-01A-02 3 0.0424 0.9249 0.008 0.000 0.992
#> TCGA-06-0173-01A-01 3 0.0592 0.9227 0.000 0.012 0.988
#> TCGA-06-0179-01A-02 2 0.5327 0.6172 0.000 0.728 0.272
#> TCGA-06-0182-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.4121 0.8115 0.832 0.000 0.168
#> TCGA-06-0208-01B-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 3 0.1529 0.9037 0.000 0.040 0.960
#> TCGA-06-0219-01A-01 3 0.0237 0.9271 0.004 0.000 0.996
#> TCGA-06-0221-01A-01 1 0.3412 0.8585 0.876 0.000 0.124
#> TCGA-06-0237-01A-02 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 1 0.4178 0.8062 0.828 0.000 0.172
#> TCGA-08-0349-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 3 0.4605 0.7402 0.000 0.204 0.796
#> TCGA-08-0386-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-08-0520-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0009-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0016-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0021-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0023-01B-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0027-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0038-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0043-01A-01 3 0.2711 0.8570 0.088 0.000 0.912
#> TCGA-02-0070-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0102-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0260-01A-03 3 0.3412 0.8200 0.124 0.000 0.876
#> TCGA-02-0269-01B-01 3 0.0237 0.9271 0.004 0.000 0.996
#> TCGA-02-0285-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0289-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0290-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0317-01A-01 3 0.0237 0.9271 0.004 0.000 0.996
#> TCGA-02-0333-01A-02 3 0.0237 0.9271 0.004 0.000 0.996
#> TCGA-02-0422-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0430-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0125-01A-01 3 0.0237 0.9271 0.004 0.000 0.996
#> TCGA-06-0126-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0137-01A-03 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0145-01A-04 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0148-01A-01 3 0.0237 0.9270 0.000 0.004 0.996
#> TCGA-06-0187-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0211-01B-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0402-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-08-0246-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-08-0354-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-08-0355-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-08-0357-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-08-0358-01A-01 3 0.0237 0.9271 0.004 0.000 0.996
#> TCGA-08-0375-01A-01 3 0.0237 0.9271 0.004 0.000 0.996
#> TCGA-08-0511-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-08-0514-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-08-0518-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-08-0529-01A-02 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-08-0531-01A-01 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-02-0057-01A-01 3 0.4399 0.7606 0.000 0.188 0.812
#> TCGA-02-0004-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.1031 0.9551 0.000 0.976 0.024
#> TCGA-02-0025-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0054-01A-01 2 0.4504 0.7571 0.000 0.804 0.196
#> TCGA-02-0055-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0079-01A-03 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0085-01A-01 2 0.1031 0.9551 0.000 0.976 0.024
#> TCGA-02-0086-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0099-01A-01 2 0.1163 0.9519 0.000 0.972 0.028
#> TCGA-02-0106-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-02-0326-01A-01 3 0.0237 0.9271 0.004 0.000 0.996
#> TCGA-02-0337-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0122-01A-01 2 0.1031 0.9548 0.000 0.976 0.024
#> TCGA-06-0124-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0143-01A-01 2 0.1031 0.9548 0.000 0.976 0.024
#> TCGA-06-0147-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 3 0.6305 0.0815 0.000 0.484 0.516
#> TCGA-06-0152-01A-02 3 0.0000 0.9288 0.000 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 3 0.6192 0.3068 0.000 0.420 0.580
#> TCGA-06-0176-01A-03 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.2356 0.9088 0.000 0.928 0.072
#> TCGA-06-0189-01A-05 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0412-01A-01 2 0.1529 0.9416 0.000 0.960 0.040
#> TCGA-06-0644-01A-02 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-08-0352-01A-01 2 0.0892 0.9576 0.000 0.980 0.020
#> TCGA-08-0360-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-08-0392-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9709 0.000 1.000 0.000
#> TCGA-12-0620-01A-01 2 0.6079 0.3617 0.000 0.612 0.388
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.2345 0.879 0.900 0.000 0.000 0.100
#> TCGA-02-0010-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.2216 0.889 0.908 0.000 0.000 0.092
#> TCGA-02-0047-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-02-0048-01A-01 1 0.3726 0.723 0.788 0.000 0.212 0.000
#> TCGA-02-0060-01A-01 4 0.2589 0.850 0.116 0.000 0.000 0.884
#> TCGA-02-0069-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0084-01A-03 4 0.4356 0.553 0.000 0.000 0.292 0.708
#> TCGA-02-0087-01A-01 4 0.6396 0.385 0.360 0.000 0.076 0.564
#> TCGA-02-0104-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.3448 0.787 0.004 0.000 0.828 0.168
#> TCGA-02-0325-01A-01 1 0.3610 0.752 0.800 0.000 0.200 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0439-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-02-0440-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0128-01A-01 4 0.4585 0.541 0.332 0.000 0.000 0.668
#> TCGA-06-0129-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-06-0156-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0166-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0174-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-06-0238-01A-02 4 0.4830 0.406 0.392 0.000 0.000 0.608
#> TCGA-06-0241-01A-02 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0648-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-08-0348-01A-01 1 0.0469 0.971 0.988 0.000 0.000 0.012
#> TCGA-08-0350-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-08-0353-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0359-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-08-0385-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.982 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-02-0113-01A-01 3 0.4605 0.529 0.000 0.000 0.664 0.336
#> TCGA-02-0115-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-02-0451-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0132-01A-02 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0133-01A-02 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 4 0.2408 0.862 0.104 0.000 0.000 0.896
#> TCGA-06-0162-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 4 0.2408 0.862 0.104 0.000 0.000 0.896
#> TCGA-06-0171-01A-02 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0179-01A-02 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 3 0.4605 0.529 0.000 0.000 0.664 0.336
#> TCGA-06-0185-01A-01 3 0.4605 0.529 0.000 0.000 0.664 0.336
#> TCGA-06-0195-01B-01 4 0.0188 0.942 0.004 0.000 0.000 0.996
#> TCGA-06-0208-01B-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 4 0.2408 0.862 0.104 0.000 0.000 0.896
#> TCGA-06-0237-01A-02 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-08-0349-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-08-0386-01A-01 3 0.4985 0.216 0.000 0.000 0.532 0.468
#> TCGA-08-0520-01A-01 4 0.1211 0.909 0.000 0.000 0.040 0.960
#> TCGA-02-0007-01A-01 3 0.3219 0.789 0.000 0.000 0.836 0.164
#> TCGA-02-0009-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0016-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0021-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0027-01A-01 3 0.2281 0.862 0.000 0.000 0.904 0.096
#> TCGA-02-0038-01A-01 3 0.4998 0.151 0.000 0.000 0.512 0.488
#> TCGA-02-0043-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-06-0137-01A-03 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0354-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0357-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0358-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0375-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0057-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.3942 0.728 0.000 0.764 0.000 0.236
#> TCGA-02-0025-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0921 0.953 0.000 0.972 0.000 0.028
#> TCGA-02-0051-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.3975 0.722 0.000 0.760 0.000 0.240
#> TCGA-02-0055-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0079-01A-03 2 0.0469 0.963 0.000 0.988 0.000 0.012
#> TCGA-02-0085-01A-01 4 0.0000 0.944 0.000 0.000 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.3311 0.808 0.000 0.828 0.000 0.172
#> TCGA-02-0106-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-02-0337-01A-01 2 0.2408 0.893 0.000 0.896 0.000 0.104
#> TCGA-06-0122-01A-01 2 0.1716 0.919 0.000 0.936 0.064 0.000
#> TCGA-06-0124-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 2 0.1824 0.921 0.000 0.936 0.060 0.004
#> TCGA-06-0147-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.2345 0.897 0.000 0.900 0.000 0.100
#> TCGA-06-0152-01A-02 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> TCGA-06-0154-01A-02 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.2408 0.893 0.000 0.896 0.000 0.104
#> TCGA-06-0176-01A-03 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.2408 0.893 0.000 0.896 0.000 0.104
#> TCGA-06-0189-01A-05 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-08-0352-01A-01 2 0.0817 0.956 0.000 0.976 0.000 0.024
#> TCGA-08-0360-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.1792 0.924 0.000 0.932 0.000 0.068
#> TCGA-08-0392-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.970 0.000 1.000 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.3764 0.733 0.000 0.784 0.216 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.4504 0.6467 0.748 0.000 0.000 0.084 0.168
#> TCGA-02-0010-01A-01 1 0.0000 0.8146 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.3932 0.5285 0.672 0.000 0.000 0.000 0.328
#> TCGA-02-0014-01A-01 1 0.0000 0.8146 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0609 0.8146 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0026-01B-01 1 0.0290 0.8151 0.992 0.000 0.000 0.000 0.008
#> TCGA-02-0028-01A-01 1 0.0000 0.8146 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.4409 0.6646 0.752 0.000 0.000 0.072 0.176
#> TCGA-02-0047-01A-01 4 0.3169 0.6352 0.000 0.004 0.016 0.840 0.140
#> TCGA-02-0048-01A-01 1 0.6113 0.2205 0.572 0.000 0.308 0.016 0.104
#> TCGA-02-0060-01A-01 4 0.5847 -0.1696 0.096 0.000 0.000 0.480 0.424
#> TCGA-02-0069-01A-01 1 0.0000 0.8146 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.2852 0.7718 0.828 0.000 0.000 0.000 0.172
#> TCGA-02-0080-01A-01 1 0.3837 0.4535 0.692 0.000 0.000 0.000 0.308
#> TCGA-02-0084-01A-03 5 0.6889 0.1090 0.000 0.120 0.040 0.384 0.456
#> TCGA-02-0087-01A-01 5 0.6801 0.5905 0.244 0.000 0.008 0.280 0.468
#> TCGA-02-0104-01A-01 1 0.0000 0.8146 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.8146 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.8146 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.7037 -0.0555 0.008 0.000 0.372 0.316 0.304
#> TCGA-02-0325-01A-01 5 0.6038 -0.0839 0.444 0.000 0.100 0.004 0.452
#> TCGA-02-0338-01A-01 1 0.0000 0.8146 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.8146 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.3816 0.4623 0.696 0.000 0.000 0.000 0.304
#> TCGA-02-0439-01A-01 4 0.4610 0.2329 0.000 0.000 0.016 0.596 0.388
#> TCGA-02-0440-01A-01 1 0.2970 0.7711 0.828 0.000 0.000 0.004 0.168
#> TCGA-02-0446-01A-01 4 0.3169 0.6357 0.000 0.004 0.016 0.840 0.140
#> TCGA-06-0128-01A-01 5 0.6813 0.5654 0.316 0.000 0.000 0.320 0.364
#> TCGA-06-0129-01A-01 1 0.1851 0.8052 0.912 0.000 0.000 0.000 0.088
#> TCGA-06-0146-01A-01 1 0.3752 0.4811 0.708 0.000 0.000 0.000 0.292
#> TCGA-06-0156-01A-01 4 0.3351 0.6239 0.000 0.004 0.020 0.828 0.148
#> TCGA-06-0166-01A-01 4 0.3474 0.6233 0.000 0.008 0.020 0.824 0.148
#> TCGA-06-0174-01A-01 1 0.2930 0.7733 0.832 0.000 0.000 0.004 0.164
#> TCGA-06-0177-01A-01 1 0.2813 0.7743 0.832 0.000 0.000 0.000 0.168
#> TCGA-06-0238-01A-02 5 0.6482 0.5065 0.200 0.000 0.000 0.332 0.468
#> TCGA-06-0241-01A-02 1 0.2890 0.7762 0.836 0.000 0.000 0.004 0.160
#> TCGA-06-0410-01A-01 1 0.3013 0.7745 0.832 0.000 0.000 0.008 0.160
#> TCGA-06-0413-01A-01 1 0.0609 0.8146 0.980 0.000 0.000 0.000 0.020
#> TCGA-06-0414-01A-01 1 0.3010 0.7683 0.824 0.000 0.000 0.004 0.172
#> TCGA-06-0646-01A-01 4 0.3952 0.6091 0.000 0.032 0.024 0.812 0.132
#> TCGA-06-0648-01A-01 1 0.2891 0.7711 0.824 0.000 0.000 0.000 0.176
#> TCGA-08-0245-01A-01 1 0.1121 0.8133 0.956 0.000 0.000 0.000 0.044
#> TCGA-08-0344-01A-01 1 0.0000 0.8146 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 4 0.3351 0.6277 0.000 0.004 0.020 0.828 0.148
#> TCGA-08-0348-01A-01 1 0.4654 0.4565 0.628 0.000 0.000 0.024 0.348
#> TCGA-08-0350-01A-01 1 0.4161 0.3427 0.608 0.000 0.000 0.000 0.392
#> TCGA-08-0353-01A-01 3 0.0693 0.8987 0.000 0.000 0.980 0.008 0.012
#> TCGA-08-0359-01A-01 4 0.4298 0.3272 0.000 0.000 0.008 0.640 0.352
#> TCGA-08-0385-01A-01 1 0.0162 0.8136 0.996 0.000 0.000 0.000 0.004
#> TCGA-08-0517-01A-01 1 0.1704 0.8102 0.928 0.000 0.000 0.004 0.068
#> TCGA-08-0524-01A-01 1 0.0000 0.8146 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.2930 0.7748 0.832 0.000 0.000 0.004 0.164
#> TCGA-12-0618-01A-01 1 0.2605 0.7856 0.852 0.000 0.000 0.000 0.148
#> TCGA-02-0089-01A-01 4 0.3038 0.6109 0.000 0.088 0.016 0.872 0.024
#> TCGA-02-0113-01A-01 3 0.4626 0.4425 0.000 0.000 0.616 0.364 0.020
#> TCGA-02-0115-01A-01 4 0.1557 0.7036 0.000 0.008 0.000 0.940 0.052
#> TCGA-02-0451-01A-01 4 0.0727 0.6934 0.000 0.012 0.004 0.980 0.004
#> TCGA-06-0132-01A-02 4 0.2732 0.6725 0.000 0.000 0.000 0.840 0.160
#> TCGA-06-0133-01A-02 4 0.2732 0.6721 0.000 0.000 0.000 0.840 0.160
#> TCGA-06-0138-01A-02 4 0.1341 0.7047 0.000 0.000 0.000 0.944 0.056
#> TCGA-06-0160-01A-01 4 0.4666 0.2953 0.016 0.000 0.000 0.572 0.412
#> TCGA-06-0162-01A-01 4 0.2732 0.6722 0.000 0.000 0.000 0.840 0.160
#> TCGA-06-0167-01A-01 4 0.4666 0.2953 0.016 0.000 0.000 0.572 0.412
#> TCGA-06-0171-01A-02 4 0.2127 0.6958 0.000 0.000 0.000 0.892 0.108
#> TCGA-06-0173-01A-01 4 0.1799 0.6835 0.000 0.012 0.020 0.940 0.028
#> TCGA-06-0179-01A-02 4 0.2732 0.6725 0.000 0.000 0.000 0.840 0.160
#> TCGA-06-0182-01A-01 3 0.5080 0.3979 0.000 0.000 0.588 0.368 0.044
#> TCGA-06-0185-01A-01 3 0.4849 0.4376 0.000 0.000 0.608 0.360 0.032
#> TCGA-06-0195-01B-01 4 0.3508 0.5990 0.000 0.000 0.000 0.748 0.252
#> TCGA-06-0208-01B-01 4 0.2519 0.6938 0.000 0.000 0.016 0.884 0.100
#> TCGA-06-0214-01A-02 4 0.1074 0.6892 0.000 0.012 0.016 0.968 0.004
#> TCGA-06-0219-01A-01 4 0.2852 0.6684 0.000 0.000 0.000 0.828 0.172
#> TCGA-06-0221-01A-01 4 0.4757 0.3393 0.024 0.000 0.000 0.596 0.380
#> TCGA-06-0237-01A-02 4 0.2280 0.6960 0.000 0.000 0.000 0.880 0.120
#> TCGA-06-0240-01A-02 4 0.4060 0.4407 0.000 0.000 0.000 0.640 0.360
#> TCGA-08-0349-01A-01 4 0.1740 0.7023 0.000 0.000 0.012 0.932 0.056
#> TCGA-08-0380-01A-01 4 0.0609 0.6995 0.000 0.000 0.000 0.980 0.020
#> TCGA-08-0386-01A-01 4 0.5599 0.0551 0.000 0.000 0.444 0.484 0.072
#> TCGA-08-0520-01A-01 4 0.2659 0.6769 0.000 0.000 0.060 0.888 0.052
#> TCGA-02-0007-01A-01 3 0.5026 0.5390 0.000 0.000 0.656 0.280 0.064
#> TCGA-02-0009-01A-01 3 0.0324 0.9007 0.000 0.000 0.992 0.004 0.004
#> TCGA-02-0016-01A-01 3 0.0865 0.8963 0.000 0.000 0.972 0.004 0.024
#> TCGA-02-0021-01A-01 3 0.0290 0.9009 0.000 0.000 0.992 0.008 0.000
#> TCGA-02-0023-01B-01 3 0.1892 0.8803 0.000 0.000 0.916 0.004 0.080
#> TCGA-02-0027-01A-01 3 0.1809 0.8699 0.000 0.000 0.928 0.060 0.012
#> TCGA-02-0038-01A-01 4 0.6147 0.2561 0.000 0.084 0.312 0.576 0.028
#> TCGA-02-0043-01A-01 3 0.0000 0.9005 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.1116 0.8930 0.000 0.004 0.964 0.004 0.028
#> TCGA-02-0102-01A-01 3 0.0451 0.9009 0.000 0.000 0.988 0.004 0.008
#> TCGA-02-0260-01A-03 3 0.1908 0.8653 0.000 0.000 0.908 0.000 0.092
#> TCGA-02-0269-01B-01 3 0.1908 0.8653 0.000 0.000 0.908 0.000 0.092
#> TCGA-02-0285-01A-01 3 0.0955 0.8947 0.000 0.000 0.968 0.004 0.028
#> TCGA-02-0289-01A-01 3 0.0609 0.8960 0.000 0.000 0.980 0.000 0.020
#> TCGA-02-0290-01A-01 3 0.0880 0.8963 0.000 0.000 0.968 0.000 0.032
#> TCGA-02-0317-01A-01 3 0.1908 0.8653 0.000 0.000 0.908 0.000 0.092
#> TCGA-02-0333-01A-02 3 0.1908 0.8653 0.000 0.000 0.908 0.000 0.092
#> TCGA-02-0422-01A-01 3 0.0451 0.9007 0.000 0.000 0.988 0.008 0.004
#> TCGA-02-0430-01A-01 3 0.0451 0.9007 0.000 0.000 0.988 0.008 0.004
#> TCGA-06-0125-01A-01 3 0.0324 0.9007 0.000 0.000 0.992 0.004 0.004
#> TCGA-06-0126-01A-01 3 0.0162 0.9008 0.000 0.000 0.996 0.004 0.000
#> TCGA-06-0137-01A-03 3 0.0324 0.9007 0.000 0.000 0.992 0.004 0.004
#> TCGA-06-0145-01A-04 3 0.0693 0.8993 0.000 0.000 0.980 0.008 0.012
#> TCGA-06-0148-01A-01 3 0.0794 0.8964 0.000 0.000 0.972 0.000 0.028
#> TCGA-06-0187-01A-01 3 0.2388 0.8512 0.000 0.000 0.900 0.072 0.028
#> TCGA-06-0211-01B-01 3 0.0290 0.9009 0.000 0.000 0.992 0.008 0.000
#> TCGA-06-0402-01A-01 3 0.0290 0.9009 0.000 0.000 0.992 0.008 0.000
#> TCGA-08-0246-01A-01 3 0.5747 0.5698 0.000 0.176 0.676 0.120 0.028
#> TCGA-08-0354-01A-01 3 0.1725 0.8892 0.000 0.000 0.936 0.020 0.044
#> TCGA-08-0355-01A-01 3 0.1952 0.8791 0.000 0.000 0.912 0.004 0.084
#> TCGA-08-0357-01A-01 3 0.0451 0.9007 0.000 0.000 0.988 0.008 0.004
#> TCGA-08-0358-01A-01 3 0.2074 0.8592 0.000 0.000 0.896 0.000 0.104
#> TCGA-08-0375-01A-01 3 0.0609 0.8960 0.000 0.000 0.980 0.000 0.020
#> TCGA-08-0511-01A-01 3 0.1117 0.8949 0.000 0.000 0.964 0.016 0.020
#> TCGA-08-0514-01A-01 3 0.1216 0.8932 0.000 0.000 0.960 0.020 0.020
#> TCGA-08-0518-01A-01 3 0.0324 0.9007 0.000 0.000 0.992 0.004 0.004
#> TCGA-08-0529-01A-02 3 0.0451 0.9007 0.000 0.000 0.988 0.008 0.004
#> TCGA-08-0531-01A-01 3 0.0451 0.9008 0.000 0.000 0.988 0.008 0.004
#> TCGA-02-0057-01A-01 4 0.4843 0.3777 0.000 0.256 0.020 0.696 0.028
#> TCGA-02-0004-01A-01 2 0.3913 0.6912 0.000 0.676 0.000 0.000 0.324
#> TCGA-02-0006-01B-01 2 0.5337 0.2131 0.000 0.512 0.020 0.448 0.020
#> TCGA-02-0025-01A-01 2 0.3913 0.6912 0.000 0.676 0.000 0.000 0.324
#> TCGA-02-0033-01A-01 2 0.3895 0.6924 0.000 0.680 0.000 0.000 0.320
#> TCGA-02-0034-01A-01 2 0.3895 0.6936 0.000 0.680 0.000 0.000 0.320
#> TCGA-02-0039-01A-01 2 0.3690 0.6761 0.000 0.780 0.000 0.200 0.020
#> TCGA-02-0051-01A-01 2 0.3895 0.6924 0.000 0.680 0.000 0.000 0.320
#> TCGA-02-0054-01A-01 2 0.5560 0.2122 0.000 0.508 0.024 0.440 0.028
#> TCGA-02-0055-01A-01 2 0.3913 0.6912 0.000 0.676 0.000 0.000 0.324
#> TCGA-02-0059-01A-01 2 0.3895 0.6924 0.000 0.680 0.000 0.000 0.320
#> TCGA-02-0064-01A-01 2 0.0290 0.7825 0.000 0.992 0.000 0.000 0.008
#> TCGA-02-0075-01A-01 2 0.0290 0.7824 0.000 0.992 0.000 0.000 0.008
#> TCGA-02-0079-01A-03 2 0.3971 0.7093 0.000 0.804 0.004 0.124 0.068
#> TCGA-02-0085-01A-01 4 0.2574 0.6171 0.000 0.112 0.000 0.876 0.012
#> TCGA-02-0086-01A-01 2 0.0162 0.7827 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0099-01A-01 2 0.5315 0.2675 0.000 0.532 0.020 0.428 0.020
#> TCGA-02-0106-01A-01 2 0.3895 0.6924 0.000 0.680 0.000 0.000 0.320
#> TCGA-02-0107-01A-01 2 0.0771 0.7806 0.000 0.976 0.000 0.020 0.004
#> TCGA-02-0111-01A-01 2 0.0404 0.7811 0.000 0.988 0.000 0.012 0.000
#> TCGA-02-0326-01A-01 3 0.3884 0.6498 0.000 0.000 0.708 0.004 0.288
#> TCGA-02-0337-01A-01 2 0.4026 0.6342 0.000 0.736 0.000 0.244 0.020
#> TCGA-06-0122-01A-01 2 0.4558 0.6876 0.000 0.780 0.076 0.120 0.024
#> TCGA-06-0124-01A-01 2 0.0290 0.7820 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0130-01A-01 2 0.3913 0.6912 0.000 0.676 0.000 0.000 0.324
#> TCGA-06-0139-01A-01 2 0.3730 0.7078 0.000 0.712 0.000 0.000 0.288
#> TCGA-06-0143-01A-01 2 0.4423 0.6892 0.000 0.784 0.048 0.140 0.028
#> TCGA-06-0147-01A-01 2 0.2074 0.7701 0.000 0.896 0.000 0.000 0.104
#> TCGA-06-0149-01A-05 2 0.5693 0.3852 0.000 0.572 0.028 0.360 0.040
#> TCGA-06-0152-01A-02 3 0.2488 0.8553 0.000 0.000 0.872 0.004 0.124
#> TCGA-06-0154-01A-02 2 0.0404 0.7827 0.000 0.988 0.000 0.000 0.012
#> TCGA-06-0164-01A-01 2 0.0510 0.7824 0.000 0.984 0.000 0.000 0.016
#> TCGA-06-0175-01A-01 2 0.5745 0.3446 0.000 0.552 0.040 0.380 0.028
#> TCGA-06-0176-01A-03 2 0.3895 0.6924 0.000 0.680 0.000 0.000 0.320
#> TCGA-06-0184-01A-01 2 0.4707 0.3843 0.000 0.588 0.000 0.392 0.020
#> TCGA-06-0189-01A-05 2 0.3366 0.7304 0.000 0.768 0.000 0.000 0.232
#> TCGA-06-0190-01A-01 2 0.1043 0.7797 0.000 0.960 0.000 0.000 0.040
#> TCGA-06-0194-01A-01 2 0.0162 0.7827 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0197-01A-02 2 0.2648 0.7578 0.000 0.848 0.000 0.000 0.152
#> TCGA-06-0210-01A-01 2 0.1403 0.7739 0.000 0.952 0.000 0.024 0.024
#> TCGA-06-0397-01A-01 2 0.2516 0.7627 0.000 0.860 0.000 0.000 0.140
#> TCGA-06-0409-01A-02 2 0.0807 0.7801 0.000 0.976 0.000 0.012 0.012
#> TCGA-06-0412-01A-01 2 0.3584 0.7312 0.000 0.848 0.040 0.084 0.028
#> TCGA-06-0644-01A-02 2 0.3895 0.6924 0.000 0.680 0.000 0.000 0.320
#> TCGA-06-0645-01A-01 2 0.2110 0.7616 0.000 0.912 0.000 0.072 0.016
#> TCGA-08-0346-01A-01 2 0.0671 0.7800 0.000 0.980 0.000 0.016 0.004
#> TCGA-08-0352-01A-01 2 0.4487 0.6746 0.000 0.768 0.036 0.168 0.028
#> TCGA-08-0360-01A-01 2 0.0566 0.7813 0.000 0.984 0.000 0.012 0.004
#> TCGA-08-0390-01A-01 2 0.2909 0.7302 0.000 0.848 0.000 0.140 0.012
#> TCGA-08-0392-01A-01 2 0.3895 0.6924 0.000 0.680 0.000 0.000 0.320
#> TCGA-08-0509-01A-01 2 0.2006 0.7637 0.000 0.916 0.000 0.072 0.012
#> TCGA-08-0510-01A-01 2 0.2839 0.7530 0.000 0.892 0.036 0.048 0.024
#> TCGA-08-0512-01A-01 2 0.2648 0.7585 0.000 0.848 0.000 0.000 0.152
#> TCGA-08-0522-01A-01 2 0.3895 0.6924 0.000 0.680 0.000 0.000 0.320
#> TCGA-12-0619-01A-01 2 0.0290 0.7824 0.000 0.992 0.000 0.000 0.008
#> TCGA-12-0620-01A-01 2 0.5574 0.6107 0.000 0.712 0.136 0.100 0.052
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.4837 0.55884 0.616 0.000 0.000 0.004 0.312 0.068
#> TCGA-02-0010-01A-01 1 0.0260 0.76886 0.992 0.000 0.000 0.000 0.008 0.000
#> TCGA-02-0011-01B-01 5 0.4936 0.11329 0.436 0.000 0.000 0.064 0.500 0.000
#> TCGA-02-0014-01A-01 1 0.0260 0.76886 0.992 0.000 0.000 0.000 0.008 0.000
#> TCGA-02-0024-01B-01 1 0.0713 0.76993 0.972 0.000 0.000 0.000 0.028 0.000
#> TCGA-02-0026-01B-01 1 0.0260 0.76886 0.992 0.000 0.000 0.000 0.008 0.000
#> TCGA-02-0028-01A-01 1 0.0260 0.76886 0.992 0.000 0.000 0.000 0.008 0.000
#> TCGA-02-0046-01A-01 1 0.4772 0.57371 0.624 0.000 0.000 0.004 0.308 0.064
#> TCGA-02-0047-01A-01 6 0.4246 0.49527 0.000 0.028 0.000 0.012 0.268 0.692
#> TCGA-02-0048-01A-01 1 0.6721 0.15457 0.452 0.000 0.308 0.012 0.196 0.032
#> TCGA-02-0060-01A-01 5 0.5974 0.41468 0.064 0.000 0.000 0.112 0.592 0.232
#> TCGA-02-0069-01A-01 1 0.0146 0.76998 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0074-01A-01 1 0.3547 0.68104 0.696 0.000 0.000 0.000 0.300 0.004
#> TCGA-02-0080-01A-01 5 0.5205 0.36213 0.412 0.000 0.000 0.092 0.496 0.000
#> TCGA-02-0084-01A-03 5 0.5747 0.39848 0.000 0.076 0.004 0.096 0.648 0.176
#> TCGA-02-0087-01A-01 5 0.5764 0.55731 0.120 0.004 0.004 0.092 0.668 0.112
#> TCGA-02-0104-01A-01 1 0.0260 0.76886 0.992 0.000 0.000 0.000 0.008 0.000
#> TCGA-02-0114-01A-01 1 0.0260 0.76886 0.992 0.000 0.000 0.000 0.008 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.77096 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.6977 0.00566 0.004 0.028 0.152 0.036 0.460 0.320
#> TCGA-02-0325-01A-01 5 0.4987 0.40869 0.268 0.000 0.020 0.056 0.652 0.004
#> TCGA-02-0338-01A-01 1 0.0000 0.77096 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.77096 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 5 0.5205 0.36213 0.412 0.000 0.000 0.092 0.496 0.000
#> TCGA-02-0439-01A-01 5 0.4693 0.15576 0.000 0.004 0.000 0.040 0.564 0.392
#> TCGA-02-0440-01A-01 1 0.3665 0.68151 0.696 0.000 0.000 0.004 0.296 0.004
#> TCGA-02-0446-01A-01 6 0.4267 0.49093 0.000 0.028 0.000 0.012 0.272 0.688
#> TCGA-06-0128-01A-01 5 0.6111 0.55000 0.160 0.000 0.000 0.068 0.592 0.180
#> TCGA-06-0129-01A-01 1 0.3720 0.64887 0.736 0.000 0.000 0.028 0.236 0.000
#> TCGA-06-0146-01A-01 5 0.5178 0.34340 0.424 0.000 0.000 0.088 0.488 0.000
#> TCGA-06-0156-01A-01 6 0.4245 0.48155 0.000 0.020 0.008 0.008 0.268 0.696
#> TCGA-06-0166-01A-01 6 0.4465 0.48449 0.000 0.032 0.008 0.008 0.268 0.684
#> TCGA-06-0174-01A-01 1 0.3489 0.69196 0.708 0.000 0.000 0.000 0.288 0.004
#> TCGA-06-0177-01A-01 1 0.3489 0.68996 0.708 0.000 0.000 0.000 0.288 0.004
#> TCGA-06-0238-01A-02 5 0.6129 0.48534 0.152 0.000 0.000 0.068 0.588 0.192
#> TCGA-06-0241-01A-02 1 0.3448 0.69839 0.716 0.000 0.000 0.000 0.280 0.004
#> TCGA-06-0410-01A-01 1 0.3555 0.69643 0.712 0.000 0.000 0.000 0.280 0.008
#> TCGA-06-0413-01A-01 1 0.0713 0.76993 0.972 0.000 0.000 0.000 0.028 0.000
#> TCGA-06-0414-01A-01 1 0.3547 0.68104 0.696 0.000 0.000 0.000 0.300 0.004
#> TCGA-06-0646-01A-01 6 0.5043 0.49520 0.000 0.068 0.016 0.008 0.244 0.664
#> TCGA-06-0648-01A-01 1 0.3565 0.67219 0.692 0.000 0.000 0.000 0.304 0.004
#> TCGA-08-0245-01A-01 1 0.1910 0.76055 0.892 0.000 0.000 0.000 0.108 0.000
#> TCGA-08-0344-01A-01 1 0.0260 0.76886 0.992 0.000 0.000 0.000 0.008 0.000
#> TCGA-08-0347-01A-01 6 0.4495 0.46741 0.000 0.028 0.008 0.008 0.288 0.668
#> TCGA-08-0348-01A-01 5 0.5183 0.07224 0.388 0.000 0.000 0.004 0.528 0.080
#> TCGA-08-0350-01A-01 5 0.4601 0.41725 0.312 0.000 0.000 0.060 0.628 0.000
#> TCGA-08-0353-01A-01 3 0.1152 0.86099 0.000 0.000 0.952 0.000 0.044 0.004
#> TCGA-08-0359-01A-01 6 0.4300 0.14382 0.000 0.004 0.000 0.012 0.456 0.528
#> TCGA-08-0385-01A-01 1 0.0790 0.75976 0.968 0.000 0.000 0.000 0.032 0.000
#> TCGA-08-0517-01A-01 1 0.2738 0.74036 0.820 0.000 0.000 0.000 0.176 0.004
#> TCGA-08-0524-01A-01 1 0.0000 0.77096 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.3555 0.69643 0.712 0.000 0.000 0.000 0.280 0.008
#> TCGA-12-0618-01A-01 1 0.3426 0.69858 0.720 0.000 0.000 0.000 0.276 0.004
#> TCGA-02-0089-01A-01 6 0.2896 0.61174 0.000 0.140 0.004 0.004 0.012 0.840
#> TCGA-02-0113-01A-01 3 0.5021 0.31048 0.000 0.000 0.536 0.024 0.032 0.408
#> TCGA-02-0115-01A-01 6 0.2699 0.65687 0.000 0.040 0.000 0.028 0.048 0.884
#> TCGA-02-0451-01A-01 6 0.1801 0.65504 0.000 0.056 0.000 0.004 0.016 0.924
#> TCGA-06-0132-01A-02 6 0.4880 0.55533 0.000 0.020 0.000 0.164 0.116 0.700
#> TCGA-06-0133-01A-02 6 0.4451 0.55736 0.000 0.004 0.000 0.148 0.124 0.724
#> TCGA-06-0138-01A-02 6 0.1777 0.66075 0.000 0.012 0.000 0.032 0.024 0.932
#> TCGA-06-0160-01A-01 5 0.6024 -0.03400 0.000 0.000 0.000 0.244 0.388 0.368
#> TCGA-06-0162-01A-01 6 0.4411 0.55856 0.000 0.004 0.000 0.148 0.120 0.728
#> TCGA-06-0167-01A-01 5 0.6024 -0.03400 0.000 0.000 0.000 0.244 0.388 0.368
#> TCGA-06-0171-01A-02 6 0.2420 0.64291 0.000 0.000 0.000 0.076 0.040 0.884
#> TCGA-06-0173-01A-01 6 0.2465 0.64496 0.000 0.040 0.008 0.004 0.052 0.896
#> TCGA-06-0179-01A-02 6 0.4710 0.55349 0.000 0.012 0.000 0.164 0.116 0.708
#> TCGA-06-0182-01A-01 3 0.5317 0.31938 0.000 0.000 0.536 0.056 0.024 0.384
#> TCGA-06-0185-01A-01 3 0.5109 0.35400 0.000 0.000 0.552 0.036 0.028 0.384
#> TCGA-06-0195-01B-01 6 0.5322 0.42788 0.000 0.000 0.000 0.188 0.216 0.596
#> TCGA-06-0208-01B-01 6 0.2937 0.63469 0.000 0.000 0.020 0.080 0.036 0.864
#> TCGA-06-0214-01A-02 6 0.2032 0.64963 0.000 0.068 0.004 0.004 0.012 0.912
#> TCGA-06-0219-01A-01 6 0.4390 0.55267 0.000 0.000 0.000 0.148 0.132 0.720
#> TCGA-06-0221-01A-01 6 0.5940 0.13927 0.004 0.000 0.000 0.192 0.348 0.456
#> TCGA-06-0237-01A-02 6 0.2658 0.63770 0.000 0.000 0.008 0.080 0.036 0.876
#> TCGA-06-0240-01A-02 6 0.5859 0.22375 0.000 0.000 0.000 0.232 0.288 0.480
#> TCGA-08-0349-01A-01 6 0.1707 0.65039 0.000 0.000 0.004 0.012 0.056 0.928
#> TCGA-08-0380-01A-01 6 0.1592 0.65918 0.000 0.032 0.000 0.008 0.020 0.940
#> TCGA-08-0386-01A-01 6 0.5854 0.23855 0.000 0.000 0.356 0.016 0.132 0.496
#> TCGA-08-0520-01A-01 6 0.2722 0.63971 0.000 0.008 0.048 0.020 0.036 0.888
#> TCGA-02-0007-01A-01 3 0.5573 0.39186 0.000 0.000 0.568 0.016 0.116 0.300
#> TCGA-02-0009-01A-01 3 0.0603 0.86822 0.000 0.000 0.980 0.004 0.016 0.000
#> TCGA-02-0016-01A-01 3 0.1492 0.86336 0.000 0.000 0.940 0.024 0.036 0.000
#> TCGA-02-0021-01A-01 3 0.0748 0.86918 0.000 0.000 0.976 0.004 0.016 0.004
#> TCGA-02-0023-01B-01 3 0.3092 0.84203 0.000 0.000 0.852 0.044 0.088 0.016
#> TCGA-02-0027-01A-01 3 0.2288 0.83944 0.000 0.000 0.900 0.016 0.016 0.068
#> TCGA-02-0038-01A-01 6 0.5575 0.43694 0.000 0.108 0.204 0.004 0.040 0.644
#> TCGA-02-0043-01A-01 3 0.1003 0.86940 0.000 0.000 0.964 0.020 0.016 0.000
#> TCGA-02-0070-01A-01 3 0.2187 0.85232 0.000 0.024 0.912 0.024 0.040 0.000
#> TCGA-02-0102-01A-01 3 0.0984 0.86791 0.000 0.008 0.968 0.012 0.012 0.000
#> TCGA-02-0260-01A-03 3 0.3493 0.79655 0.000 0.000 0.800 0.064 0.136 0.000
#> TCGA-02-0269-01B-01 3 0.3493 0.79655 0.000 0.000 0.800 0.064 0.136 0.000
#> TCGA-02-0285-01A-01 3 0.2093 0.85241 0.000 0.020 0.920 0.020 0.036 0.004
#> TCGA-02-0289-01A-01 3 0.1575 0.86283 0.000 0.000 0.936 0.032 0.032 0.000
#> TCGA-02-0290-01A-01 3 0.2836 0.85114 0.000 0.016 0.872 0.052 0.060 0.000
#> TCGA-02-0317-01A-01 3 0.3435 0.79681 0.000 0.000 0.804 0.060 0.136 0.000
#> TCGA-02-0333-01A-02 3 0.3493 0.79655 0.000 0.000 0.800 0.064 0.136 0.000
#> TCGA-02-0422-01A-01 3 0.0551 0.86860 0.000 0.000 0.984 0.004 0.008 0.004
#> TCGA-02-0430-01A-01 3 0.0767 0.86796 0.000 0.000 0.976 0.008 0.012 0.004
#> TCGA-06-0125-01A-01 3 0.0692 0.86788 0.000 0.000 0.976 0.004 0.020 0.000
#> TCGA-06-0126-01A-01 3 0.0603 0.86822 0.000 0.000 0.980 0.004 0.016 0.000
#> TCGA-06-0137-01A-03 3 0.0777 0.86790 0.000 0.000 0.972 0.004 0.024 0.000
#> TCGA-06-0145-01A-04 3 0.1148 0.86683 0.000 0.000 0.960 0.020 0.016 0.004
#> TCGA-06-0148-01A-01 3 0.2711 0.85519 0.000 0.016 0.880 0.056 0.048 0.000
#> TCGA-06-0187-01A-01 3 0.3656 0.79832 0.000 0.020 0.832 0.020 0.044 0.084
#> TCGA-06-0211-01B-01 3 0.0603 0.86874 0.000 0.000 0.980 0.000 0.016 0.004
#> TCGA-06-0402-01A-01 3 0.0653 0.86882 0.000 0.000 0.980 0.012 0.004 0.004
#> TCGA-08-0246-01A-01 3 0.6561 0.36908 0.000 0.268 0.532 0.020 0.044 0.136
#> TCGA-08-0354-01A-01 3 0.3940 0.82649 0.000 0.032 0.824 0.044 0.056 0.044
#> TCGA-08-0355-01A-01 3 0.3092 0.84203 0.000 0.000 0.852 0.044 0.088 0.016
#> TCGA-08-0357-01A-01 3 0.0748 0.86834 0.000 0.000 0.976 0.004 0.016 0.004
#> TCGA-08-0358-01A-01 3 0.3513 0.79123 0.000 0.000 0.796 0.060 0.144 0.000
#> TCGA-08-0375-01A-01 3 0.1572 0.86154 0.000 0.000 0.936 0.036 0.028 0.000
#> TCGA-08-0511-01A-01 3 0.1799 0.86119 0.000 0.008 0.936 0.024 0.016 0.016
#> TCGA-08-0514-01A-01 3 0.2400 0.84818 0.000 0.020 0.908 0.020 0.036 0.016
#> TCGA-08-0518-01A-01 3 0.1053 0.86976 0.000 0.004 0.964 0.012 0.020 0.000
#> TCGA-08-0529-01A-02 3 0.0767 0.86796 0.000 0.000 0.976 0.008 0.012 0.004
#> TCGA-08-0531-01A-01 3 0.0692 0.86925 0.000 0.000 0.976 0.000 0.020 0.004
#> TCGA-02-0057-01A-01 6 0.4602 0.26664 0.000 0.364 0.008 0.004 0.024 0.600
#> TCGA-02-0004-01A-01 4 0.3841 0.98417 0.000 0.380 0.000 0.616 0.004 0.000
#> TCGA-02-0006-01B-01 2 0.4609 0.19152 0.000 0.520 0.004 0.008 0.016 0.452
#> TCGA-02-0025-01A-01 4 0.3841 0.98450 0.000 0.380 0.000 0.616 0.004 0.000
#> TCGA-02-0033-01A-01 4 0.3841 0.98752 0.000 0.380 0.000 0.616 0.004 0.000
#> TCGA-02-0034-01A-01 4 0.3955 0.97629 0.000 0.384 0.000 0.608 0.008 0.000
#> TCGA-02-0039-01A-01 2 0.3329 0.63675 0.000 0.796 0.000 0.012 0.012 0.180
#> TCGA-02-0051-01A-01 4 0.3945 0.98761 0.000 0.380 0.000 0.612 0.008 0.000
#> TCGA-02-0054-01A-01 6 0.5152 -0.08401 0.000 0.456 0.016 0.008 0.032 0.488
#> TCGA-02-0055-01A-01 4 0.3695 0.98784 0.000 0.376 0.000 0.624 0.000 0.000
#> TCGA-02-0059-01A-01 4 0.3706 0.98855 0.000 0.380 0.000 0.620 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.1858 0.62988 0.000 0.912 0.000 0.076 0.012 0.000
#> TCGA-02-0075-01A-01 2 0.2311 0.60201 0.000 0.880 0.000 0.104 0.016 0.000
#> TCGA-02-0079-01A-03 2 0.3901 0.64779 0.000 0.804 0.000 0.036 0.076 0.084
#> TCGA-02-0085-01A-01 6 0.3730 0.56824 0.000 0.192 0.000 0.008 0.032 0.768
#> TCGA-02-0086-01A-01 2 0.1895 0.63582 0.000 0.912 0.000 0.072 0.016 0.000
#> TCGA-02-0099-01A-01 2 0.4621 0.13682 0.000 0.496 0.004 0.008 0.016 0.476
#> TCGA-02-0106-01A-01 4 0.3945 0.98761 0.000 0.380 0.000 0.612 0.008 0.000
#> TCGA-02-0107-01A-01 2 0.1750 0.66814 0.000 0.932 0.000 0.040 0.012 0.016
#> TCGA-02-0111-01A-01 2 0.0790 0.66688 0.000 0.968 0.000 0.032 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.5439 0.28927 0.000 0.000 0.472 0.120 0.408 0.000
#> TCGA-02-0337-01A-01 2 0.4373 0.54767 0.000 0.688 0.000 0.008 0.044 0.260
#> TCGA-06-0122-01A-01 2 0.4451 0.63390 0.000 0.784 0.072 0.024 0.036 0.084
#> TCGA-06-0124-01A-01 2 0.1672 0.65296 0.000 0.932 0.004 0.048 0.016 0.000
#> TCGA-06-0130-01A-01 4 0.3945 0.98238 0.000 0.380 0.000 0.612 0.008 0.000
#> TCGA-06-0139-01A-01 2 0.4185 -0.75030 0.000 0.496 0.000 0.492 0.012 0.000
#> TCGA-06-0143-01A-01 2 0.4410 0.63970 0.000 0.784 0.048 0.024 0.040 0.104
#> TCGA-06-0147-01A-01 2 0.3071 0.44609 0.000 0.804 0.000 0.180 0.016 0.000
#> TCGA-06-0149-01A-05 2 0.5492 0.46441 0.000 0.612 0.028 0.020 0.048 0.292
#> TCGA-06-0152-01A-02 3 0.4555 0.78083 0.000 0.020 0.744 0.072 0.156 0.008
#> TCGA-06-0154-01A-02 2 0.2011 0.64407 0.000 0.912 0.004 0.064 0.020 0.000
#> TCGA-06-0164-01A-01 2 0.1970 0.61374 0.000 0.900 0.000 0.092 0.008 0.000
#> TCGA-06-0175-01A-01 2 0.5191 0.52002 0.000 0.648 0.032 0.016 0.036 0.268
#> TCGA-06-0176-01A-03 4 0.3706 0.98855 0.000 0.380 0.000 0.620 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.3910 0.48389 0.000 0.660 0.000 0.004 0.008 0.328
#> TCGA-06-0189-01A-05 2 0.4039 -0.52869 0.000 0.568 0.000 0.424 0.008 0.000
#> TCGA-06-0190-01A-01 2 0.2431 0.55746 0.000 0.860 0.000 0.132 0.008 0.000
#> TCGA-06-0194-01A-01 2 0.1753 0.62450 0.000 0.912 0.000 0.084 0.004 0.000
#> TCGA-06-0197-01A-02 2 0.3426 0.11286 0.000 0.720 0.000 0.276 0.004 0.000
#> TCGA-06-0210-01A-01 2 0.2019 0.67794 0.000 0.924 0.004 0.020 0.032 0.020
#> TCGA-06-0397-01A-01 2 0.3645 0.29281 0.000 0.740 0.000 0.236 0.024 0.000
#> TCGA-06-0409-01A-02 2 0.1307 0.66994 0.000 0.952 0.000 0.032 0.008 0.008
#> TCGA-06-0412-01A-01 2 0.3832 0.65244 0.000 0.828 0.048 0.020 0.044 0.060
#> TCGA-06-0644-01A-02 4 0.3945 0.98761 0.000 0.380 0.000 0.612 0.008 0.000
#> TCGA-06-0645-01A-01 2 0.1563 0.68337 0.000 0.932 0.000 0.000 0.012 0.056
#> TCGA-08-0346-01A-01 2 0.1059 0.67410 0.000 0.964 0.000 0.016 0.016 0.004
#> TCGA-08-0352-01A-01 2 0.4168 0.64425 0.000 0.788 0.036 0.016 0.032 0.128
#> TCGA-08-0360-01A-01 2 0.1124 0.66469 0.000 0.956 0.000 0.036 0.008 0.000
#> TCGA-08-0390-01A-01 2 0.2611 0.66940 0.000 0.864 0.000 0.012 0.008 0.116
#> TCGA-08-0392-01A-01 4 0.3945 0.98761 0.000 0.380 0.000 0.612 0.008 0.000
#> TCGA-08-0509-01A-01 2 0.1957 0.67930 0.000 0.912 0.000 0.008 0.008 0.072
#> TCGA-08-0510-01A-01 2 0.3021 0.66849 0.000 0.876 0.040 0.020 0.024 0.040
#> TCGA-08-0512-01A-01 2 0.3445 0.23937 0.000 0.732 0.000 0.260 0.008 0.000
#> TCGA-08-0522-01A-01 4 0.3945 0.98761 0.000 0.380 0.000 0.612 0.008 0.000
#> TCGA-12-0619-01A-01 2 0.2491 0.59005 0.000 0.868 0.000 0.112 0.020 0.000
#> TCGA-12-0620-01A-01 2 0.4913 0.59235 0.000 0.756 0.096 0.040 0.052 0.056
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> SD:kmeans 165 3.07e-22 2
#> SD:kmeans 168 1.93e-50 3
#> SD:kmeans 169 9.57e-73 4
#> SD:kmeans 145 9.75e-69 5
#> SD:kmeans 128 1.34e-67 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "skmeans"]
# you can also extract it by
# res = res_list["SD:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.940 0.944 0.977 0.5028 0.498 0.498
#> 3 3 1.000 0.963 0.982 0.3216 0.747 0.535
#> 4 4 0.968 0.932 0.971 0.1233 0.868 0.632
#> 5 5 0.864 0.799 0.891 0.0496 0.940 0.773
#> 6 6 0.767 0.662 0.794 0.0423 0.990 0.953
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0048-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0084-01A-03 1 0.2236 0.941 0.964 0.036
#> TCGA-02-0087-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0104-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0325-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0128-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0166-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0174-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.9833 0.246 0.424 0.576
#> TCGA-06-0648-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0348-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0353-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0115-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.7139 0.750 0.196 0.804
#> TCGA-06-0138-01A-02 2 0.1184 0.964 0.016 0.984
#> TCGA-06-0160-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.1184 0.963 0.016 0.984
#> TCGA-06-0167-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0171-01A-02 1 0.6247 0.803 0.844 0.156
#> TCGA-06-0173-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0179-01A-02 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0185-01A-01 1 0.9460 0.421 0.636 0.364
#> TCGA-06-0195-01B-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.8555 0.612 0.280 0.720
#> TCGA-06-0214-01A-02 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0219-01A-01 1 0.9491 0.411 0.632 0.368
#> TCGA-06-0221-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0237-01A-02 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0240-01A-02 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0349-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0380-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0520-01A-01 2 0.7219 0.745 0.200 0.800
#> TCGA-02-0007-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0009-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0016-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0021-01A-01 1 0.8386 0.636 0.732 0.268
#> TCGA-02-0023-01B-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.0376 0.971 0.996 0.004
#> TCGA-02-0038-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0043-01A-01 1 0.7219 0.745 0.800 0.200
#> TCGA-02-0070-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0102-01A-01 1 0.9754 0.322 0.592 0.408
#> TCGA-02-0260-01A-03 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0269-01B-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0285-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0289-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0290-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0317-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0333-01A-02 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0422-01A-01 2 0.5408 0.848 0.124 0.876
#> TCGA-02-0430-01A-01 1 0.7950 0.684 0.760 0.240
#> TCGA-06-0125-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0126-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0137-01A-03 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0145-01A-04 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0148-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0187-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0211-01B-01 1 0.0000 0.974 1.000 0.000
#> TCGA-06-0402-01A-01 2 0.9850 0.233 0.428 0.572
#> TCGA-08-0246-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0357-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0358-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0375-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-08-0511-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0514-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0529-01A-02 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0531-01A-01 2 0.6887 0.769 0.184 0.816
#> TCGA-02-0057-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-02-0326-01A-01 1 0.0000 0.974 1.000 0.000
#> TCGA-02-0337-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0147-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.978 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.978 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.978 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-02-0048-01A-01 1 0.0424 0.971 0.992 0.000 0.008
#> TCGA-02-0060-01A-01 1 0.0237 0.975 0.996 0.000 0.004
#> TCGA-02-0069-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0084-01A-03 1 0.5397 0.613 0.720 0.280 0.000
#> TCGA-02-0087-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0104-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0325-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0439-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-02-0440-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-06-0128-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-06-0129-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-06-0166-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-06-0174-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-06-0241-01A-02 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 1 0.6307 0.510 0.660 0.328 0.012
#> TCGA-06-0648-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-08-0347-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-08-0348-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-08-0353-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-08-0359-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-08-0385-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.977 1.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.0592 0.979 0.000 0.988 0.012
#> TCGA-02-0113-01A-01 3 0.0000 0.977 0.000 0.000 1.000
#> TCGA-02-0115-01A-01 2 0.0592 0.979 0.000 0.988 0.012
#> TCGA-02-0451-01A-01 2 0.0592 0.979 0.000 0.988 0.012
#> TCGA-06-0132-01A-02 2 0.0592 0.979 0.000 0.988 0.012
#> TCGA-06-0133-01A-02 2 0.8576 0.489 0.240 0.600 0.160
#> TCGA-06-0138-01A-02 1 0.6255 0.527 0.668 0.320 0.012
#> TCGA-06-0160-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-06-0162-01A-01 2 0.1877 0.950 0.032 0.956 0.012
#> TCGA-06-0167-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-06-0171-01A-02 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-06-0173-01A-01 2 0.5659 0.648 0.248 0.740 0.012
#> TCGA-06-0179-01A-02 2 0.0592 0.979 0.000 0.988 0.012
#> TCGA-06-0182-01A-01 3 0.0000 0.977 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 3 0.0000 0.977 0.000 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-06-0208-01B-01 3 0.0000 0.977 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.0592 0.979 0.000 0.988 0.012
#> TCGA-06-0219-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-06-0221-01A-01 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-06-0237-01A-02 1 0.3752 0.833 0.856 0.000 0.144
#> TCGA-06-0240-01A-02 1 0.0592 0.972 0.988 0.000 0.012
#> TCGA-08-0349-01A-01 1 0.1411 0.955 0.964 0.000 0.036
#> TCGA-08-0380-01A-01 2 0.0592 0.979 0.000 0.988 0.012
#> TCGA-08-0386-01A-01 3 0.4235 0.786 0.176 0.000 0.824
#> TCGA-08-0520-01A-01 3 0.0000 0.977 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.5706 0.545 0.320 0.000 0.680
#> TCGA-02-0009-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0016-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0021-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0023-01B-01 3 0.0000 0.977 0.000 0.000 1.000
#> TCGA-02-0027-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0038-01A-01 3 0.2625 0.897 0.000 0.084 0.916
#> TCGA-02-0043-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0070-01A-01 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-02-0102-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0260-01A-03 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0269-01B-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0285-01A-01 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-02-0289-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0290-01A-01 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-02-0317-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0333-01A-02 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0422-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-02-0430-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-06-0125-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-06-0126-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-06-0137-01A-03 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-06-0145-01A-04 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-06-0148-01A-01 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-06-0187-01A-01 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-06-0211-01B-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-06-0402-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-08-0246-01A-01 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-08-0354-01A-01 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-08-0355-01A-01 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-08-0357-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-08-0358-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-08-0375-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-08-0511-01A-01 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-08-0514-01A-01 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-08-0518-01A-01 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-08-0529-01A-02 3 0.0592 0.982 0.012 0.000 0.988
#> TCGA-08-0531-01A-01 3 0.0237 0.979 0.004 0.000 0.996
#> TCGA-02-0057-01A-01 2 0.0592 0.979 0.000 0.988 0.012
#> TCGA-02-0004-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0054-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0079-01A-03 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0085-01A-01 2 0.0592 0.979 0.000 0.988 0.012
#> TCGA-02-0086-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0099-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0106-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-02-0326-01A-01 3 0.0892 0.976 0.020 0.000 0.980
#> TCGA-02-0337-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0122-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0124-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0143-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0152-01A-02 3 0.0592 0.978 0.000 0.012 0.988
#> TCGA-06-0154-01A-02 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0412-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-08-0352-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-08-0392-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.987 0.000 1.000 0.000
#> TCGA-12-0620-01A-01 2 0.0424 0.981 0.000 0.992 0.008
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.0336 0.96211 0.992 0.000 0.000 0.008
#> TCGA-02-0010-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-02-0048-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0084-01A-03 1 0.6275 0.48794 0.640 0.256 0.000 0.104
#> TCGA-02-0087-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0104-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0325-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0439-01A-01 4 0.4522 0.59731 0.320 0.000 0.000 0.680
#> TCGA-02-0440-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 4 0.3311 0.78962 0.172 0.000 0.000 0.828
#> TCGA-06-0128-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-06-0156-01A-01 4 0.4855 0.39634 0.400 0.000 0.000 0.600
#> TCGA-06-0166-01A-01 1 0.4522 0.47024 0.680 0.000 0.000 0.320
#> TCGA-06-0174-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 4 0.4193 0.67053 0.268 0.000 0.000 0.732
#> TCGA-06-0648-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 4 0.4164 0.67668 0.264 0.000 0.000 0.736
#> TCGA-08-0348-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-08-0353-01A-01 3 0.0707 0.94836 0.020 0.000 0.980 0.000
#> TCGA-08-0359-01A-01 4 0.4008 0.70501 0.244 0.000 0.000 0.756
#> TCGA-08-0385-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.97010 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-02-0113-01A-01 3 0.4855 0.38055 0.000 0.000 0.600 0.400
#> TCGA-02-0115-01A-01 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-02-0451-01A-01 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0132-01A-02 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0133-01A-02 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 4 0.1557 0.88709 0.056 0.000 0.000 0.944
#> TCGA-06-0162-01A-01 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 4 0.1474 0.88973 0.052 0.000 0.000 0.948
#> TCGA-06-0171-01A-02 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0179-01A-02 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 3 0.4855 0.38055 0.000 0.000 0.600 0.400
#> TCGA-06-0185-01A-01 3 0.4888 0.34967 0.000 0.000 0.588 0.412
#> TCGA-06-0195-01B-01 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0208-01B-01 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 4 0.4382 0.60401 0.296 0.000 0.000 0.704
#> TCGA-06-0237-01A-02 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-08-0349-01A-01 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 4 0.0000 0.91462 0.000 0.000 0.000 1.000
#> TCGA-08-0386-01A-01 4 0.0921 0.89733 0.000 0.000 0.028 0.972
#> TCGA-08-0520-01A-01 4 0.0469 0.90795 0.000 0.000 0.012 0.988
#> TCGA-02-0007-01A-01 1 0.5607 0.00661 0.496 0.000 0.484 0.020
#> TCGA-02-0009-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0016-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0021-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0027-01A-01 3 0.0707 0.95005 0.000 0.000 0.980 0.020
#> TCGA-02-0038-01A-01 4 0.1716 0.86703 0.000 0.000 0.064 0.936
#> TCGA-02-0043-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0070-01A-01 3 0.0707 0.94719 0.000 0.020 0.980 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-06-0137-01A-03 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-08-0354-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-08-0357-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-08-0358-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-08-0375-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-02-0057-01A-01 4 0.2868 0.81136 0.000 0.136 0.000 0.864
#> TCGA-02-0004-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0079-01A-03 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0085-01A-01 4 0.3569 0.74174 0.000 0.196 0.000 0.804
#> TCGA-02-0086-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0106-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0921 0.93962 0.028 0.000 0.972 0.000
#> TCGA-02-0337-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0122-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0124-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.96722 0.000 0.000 1.000 0.000
#> TCGA-06-0154-01A-02 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-08-0352-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-08-0392-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.0000 1.00000 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.2020 0.8156 0.900 0.000 0.000 0.000 0.100
#> TCGA-02-0010-01A-01 1 0.0162 0.8531 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0011-01B-01 1 0.4307 -0.4492 0.500 0.000 0.000 0.000 0.500
#> TCGA-02-0014-01A-01 1 0.0162 0.8531 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0024-01B-01 1 0.0794 0.8501 0.972 0.000 0.000 0.000 0.028
#> TCGA-02-0026-01B-01 1 0.0162 0.8531 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0028-01A-01 1 0.0162 0.8531 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0046-01A-01 1 0.2020 0.8156 0.900 0.000 0.000 0.000 0.100
#> TCGA-02-0047-01A-01 5 0.4437 -0.0773 0.004 0.000 0.000 0.464 0.532
#> TCGA-02-0048-01A-01 1 0.0451 0.8498 0.988 0.000 0.004 0.000 0.008
#> TCGA-02-0060-01A-01 5 0.4101 0.6100 0.332 0.000 0.000 0.004 0.664
#> TCGA-02-0069-01A-01 1 0.0162 0.8531 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0074-01A-01 1 0.2074 0.8128 0.896 0.000 0.000 0.000 0.104
#> TCGA-02-0080-01A-01 5 0.4126 0.6137 0.380 0.000 0.000 0.000 0.620
#> TCGA-02-0084-01A-03 5 0.4094 0.6653 0.180 0.020 0.000 0.020 0.780
#> TCGA-02-0087-01A-01 5 0.3534 0.6640 0.256 0.000 0.000 0.000 0.744
#> TCGA-02-0104-01A-01 1 0.0162 0.8531 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0114-01A-01 1 0.0162 0.8531 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0281-01A-01 1 0.0162 0.8531 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0321-01A-01 1 0.4171 0.3562 0.604 0.000 0.000 0.000 0.396
#> TCGA-02-0325-01A-01 5 0.4138 0.5734 0.384 0.000 0.000 0.000 0.616
#> TCGA-02-0338-01A-01 1 0.0162 0.8531 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0339-01A-01 1 0.0162 0.8531 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0432-01A-02 5 0.4126 0.6137 0.380 0.000 0.000 0.000 0.620
#> TCGA-02-0439-01A-01 5 0.3535 0.6242 0.080 0.000 0.000 0.088 0.832
#> TCGA-02-0440-01A-01 1 0.1965 0.8183 0.904 0.000 0.000 0.000 0.096
#> TCGA-02-0446-01A-01 4 0.6569 0.1659 0.272 0.000 0.000 0.472 0.256
#> TCGA-06-0128-01A-01 5 0.4256 0.5386 0.436 0.000 0.000 0.000 0.564
#> TCGA-06-0129-01A-01 1 0.1410 0.8070 0.940 0.000 0.000 0.000 0.060
#> TCGA-06-0146-01A-01 5 0.4219 0.5742 0.416 0.000 0.000 0.000 0.584
#> TCGA-06-0156-01A-01 1 0.6592 0.0534 0.460 0.000 0.000 0.300 0.240
#> TCGA-06-0166-01A-01 1 0.4964 0.5462 0.700 0.000 0.000 0.096 0.204
#> TCGA-06-0174-01A-01 1 0.1965 0.8183 0.904 0.000 0.000 0.000 0.096
#> TCGA-06-0177-01A-01 1 0.1908 0.8217 0.908 0.000 0.000 0.000 0.092
#> TCGA-06-0238-01A-02 5 0.4161 0.5234 0.392 0.000 0.000 0.000 0.608
#> TCGA-06-0241-01A-02 1 0.1908 0.8209 0.908 0.000 0.000 0.000 0.092
#> TCGA-06-0410-01A-01 1 0.0609 0.8519 0.980 0.000 0.000 0.000 0.020
#> TCGA-06-0413-01A-01 1 0.0794 0.8501 0.972 0.000 0.000 0.000 0.028
#> TCGA-06-0414-01A-01 1 0.1965 0.8183 0.904 0.000 0.000 0.000 0.096
#> TCGA-06-0646-01A-01 4 0.6672 0.1155 0.272 0.000 0.000 0.440 0.288
#> TCGA-06-0648-01A-01 1 0.2230 0.7841 0.884 0.000 0.000 0.000 0.116
#> TCGA-08-0245-01A-01 1 0.0162 0.8533 0.996 0.000 0.000 0.000 0.004
#> TCGA-08-0344-01A-01 1 0.0404 0.8493 0.988 0.000 0.000 0.000 0.012
#> TCGA-08-0347-01A-01 5 0.5290 0.3463 0.076 0.000 0.000 0.300 0.624
#> TCGA-08-0348-01A-01 1 0.4302 -0.0637 0.520 0.000 0.000 0.000 0.480
#> TCGA-08-0350-01A-01 5 0.4242 0.5509 0.428 0.000 0.000 0.000 0.572
#> TCGA-08-0353-01A-01 3 0.3684 0.5712 0.280 0.000 0.720 0.000 0.000
#> TCGA-08-0359-01A-01 5 0.4619 0.4777 0.064 0.000 0.000 0.216 0.720
#> TCGA-08-0385-01A-01 1 0.1671 0.7860 0.924 0.000 0.000 0.000 0.076
#> TCGA-08-0517-01A-01 1 0.0290 0.8515 0.992 0.000 0.000 0.000 0.008
#> TCGA-08-0524-01A-01 1 0.0162 0.8531 0.996 0.000 0.000 0.000 0.004
#> TCGA-12-0616-01A-01 1 0.0609 0.8519 0.980 0.000 0.000 0.000 0.020
#> TCGA-12-0618-01A-01 1 0.1043 0.8456 0.960 0.000 0.000 0.000 0.040
#> TCGA-02-0089-01A-01 4 0.2304 0.7682 0.000 0.008 0.000 0.892 0.100
#> TCGA-02-0113-01A-01 4 0.4760 0.2538 0.000 0.000 0.416 0.564 0.020
#> TCGA-02-0115-01A-01 4 0.1732 0.7743 0.000 0.000 0.000 0.920 0.080
#> TCGA-02-0451-01A-01 4 0.1732 0.7743 0.000 0.000 0.000 0.920 0.080
#> TCGA-06-0132-01A-02 4 0.2179 0.7605 0.000 0.000 0.000 0.888 0.112
#> TCGA-06-0133-01A-02 4 0.0290 0.7817 0.000 0.000 0.000 0.992 0.008
#> TCGA-06-0138-01A-02 4 0.1270 0.7815 0.000 0.000 0.000 0.948 0.052
#> TCGA-06-0160-01A-01 5 0.4687 0.3910 0.028 0.000 0.000 0.336 0.636
#> TCGA-06-0162-01A-01 4 0.0290 0.7817 0.000 0.000 0.000 0.992 0.008
#> TCGA-06-0167-01A-01 5 0.4624 0.3820 0.024 0.000 0.000 0.340 0.636
#> TCGA-06-0171-01A-02 4 0.0609 0.7836 0.000 0.000 0.000 0.980 0.020
#> TCGA-06-0173-01A-01 4 0.1410 0.7794 0.000 0.000 0.000 0.940 0.060
#> TCGA-06-0179-01A-02 4 0.1851 0.7719 0.000 0.000 0.000 0.912 0.088
#> TCGA-06-0182-01A-01 4 0.4528 0.2048 0.000 0.000 0.444 0.548 0.008
#> TCGA-06-0185-01A-01 4 0.4630 0.3028 0.000 0.000 0.396 0.588 0.016
#> TCGA-06-0195-01B-01 4 0.1908 0.7466 0.000 0.000 0.000 0.908 0.092
#> TCGA-06-0208-01B-01 4 0.0290 0.7820 0.000 0.000 0.000 0.992 0.008
#> TCGA-06-0214-01A-02 4 0.1908 0.7709 0.000 0.000 0.000 0.908 0.092
#> TCGA-06-0219-01A-01 4 0.0404 0.7818 0.000 0.000 0.000 0.988 0.012
#> TCGA-06-0221-01A-01 4 0.5996 0.0721 0.136 0.000 0.000 0.548 0.316
#> TCGA-06-0237-01A-02 4 0.1544 0.7593 0.000 0.000 0.000 0.932 0.068
#> TCGA-06-0240-01A-02 4 0.2230 0.7467 0.000 0.000 0.000 0.884 0.116
#> TCGA-08-0349-01A-01 4 0.0290 0.7830 0.000 0.000 0.000 0.992 0.008
#> TCGA-08-0380-01A-01 4 0.1043 0.7833 0.000 0.000 0.000 0.960 0.040
#> TCGA-08-0386-01A-01 4 0.4407 0.6866 0.028 0.000 0.084 0.796 0.092
#> TCGA-08-0520-01A-01 4 0.1956 0.7526 0.000 0.000 0.008 0.916 0.076
#> TCGA-02-0007-01A-01 1 0.6783 0.2095 0.552 0.000 0.284 0.100 0.064
#> TCGA-02-0009-01A-01 3 0.0162 0.9541 0.000 0.000 0.996 0.000 0.004
#> TCGA-02-0016-01A-01 3 0.0703 0.9512 0.000 0.000 0.976 0.000 0.024
#> TCGA-02-0021-01A-01 3 0.0000 0.9541 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.2488 0.9009 0.000 0.000 0.872 0.004 0.124
#> TCGA-02-0027-01A-01 3 0.2673 0.8761 0.016 0.000 0.892 0.016 0.076
#> TCGA-02-0038-01A-01 4 0.4093 0.7213 0.000 0.024 0.072 0.816 0.088
#> TCGA-02-0043-01A-01 3 0.0162 0.9534 0.000 0.000 0.996 0.000 0.004
#> TCGA-02-0070-01A-01 3 0.1106 0.9352 0.000 0.024 0.964 0.000 0.012
#> TCGA-02-0102-01A-01 3 0.0162 0.9534 0.000 0.000 0.996 0.000 0.004
#> TCGA-02-0260-01A-03 3 0.1851 0.9264 0.000 0.000 0.912 0.000 0.088
#> TCGA-02-0269-01B-01 3 0.1851 0.9264 0.000 0.000 0.912 0.000 0.088
#> TCGA-02-0285-01A-01 3 0.0609 0.9511 0.000 0.000 0.980 0.000 0.020
#> TCGA-02-0289-01A-01 3 0.0510 0.9529 0.000 0.000 0.984 0.000 0.016
#> TCGA-02-0290-01A-01 3 0.1671 0.9315 0.000 0.000 0.924 0.000 0.076
#> TCGA-02-0317-01A-01 3 0.1851 0.9264 0.000 0.000 0.912 0.000 0.088
#> TCGA-02-0333-01A-02 3 0.1851 0.9264 0.000 0.000 0.912 0.000 0.088
#> TCGA-02-0422-01A-01 3 0.0000 0.9541 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.9541 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0162 0.9541 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0126-01A-01 3 0.0162 0.9541 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0137-01A-03 3 0.0290 0.9539 0.000 0.000 0.992 0.000 0.008
#> TCGA-06-0145-01A-04 3 0.0000 0.9541 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.1544 0.9353 0.000 0.000 0.932 0.000 0.068
#> TCGA-06-0187-01A-01 3 0.0510 0.9499 0.000 0.000 0.984 0.000 0.016
#> TCGA-06-0211-01B-01 3 0.0162 0.9541 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0402-01A-01 3 0.0000 0.9541 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.2661 0.8842 0.000 0.052 0.896 0.008 0.044
#> TCGA-08-0354-01A-01 3 0.2570 0.9109 0.000 0.028 0.888 0.000 0.084
#> TCGA-08-0355-01A-01 3 0.2660 0.8970 0.000 0.000 0.864 0.008 0.128
#> TCGA-08-0357-01A-01 3 0.0162 0.9541 0.000 0.000 0.996 0.000 0.004
#> TCGA-08-0358-01A-01 3 0.2280 0.9051 0.000 0.000 0.880 0.000 0.120
#> TCGA-08-0375-01A-01 3 0.0162 0.9541 0.000 0.000 0.996 0.000 0.004
#> TCGA-08-0511-01A-01 3 0.0000 0.9541 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0514-01A-01 3 0.0404 0.9531 0.000 0.000 0.988 0.000 0.012
#> TCGA-08-0518-01A-01 3 0.0162 0.9542 0.000 0.000 0.996 0.000 0.004
#> TCGA-08-0529-01A-02 3 0.0000 0.9541 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.0404 0.9536 0.000 0.000 0.988 0.000 0.012
#> TCGA-02-0057-01A-01 4 0.5210 0.5597 0.000 0.184 0.000 0.684 0.132
#> TCGA-02-0004-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-02-0006-01B-01 2 0.3301 0.8509 0.000 0.848 0.000 0.072 0.080
#> TCGA-02-0025-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-02-0033-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-02-0034-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-02-0039-01A-01 2 0.0609 0.9613 0.000 0.980 0.000 0.000 0.020
#> TCGA-02-0051-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-02-0054-01A-01 2 0.2569 0.9144 0.000 0.892 0.000 0.040 0.068
#> TCGA-02-0055-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-02-0059-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-02-0064-01A-01 2 0.0510 0.9624 0.000 0.984 0.000 0.000 0.016
#> TCGA-02-0075-01A-01 2 0.0963 0.9630 0.000 0.964 0.000 0.000 0.036
#> TCGA-02-0079-01A-03 2 0.2329 0.8880 0.000 0.876 0.000 0.000 0.124
#> TCGA-02-0085-01A-01 4 0.5595 0.4473 0.000 0.252 0.000 0.624 0.124
#> TCGA-02-0086-01A-01 2 0.0609 0.9649 0.000 0.980 0.000 0.000 0.020
#> TCGA-02-0099-01A-01 2 0.2685 0.9219 0.000 0.880 0.000 0.028 0.092
#> TCGA-02-0106-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-02-0107-01A-01 2 0.0609 0.9613 0.000 0.980 0.000 0.000 0.020
#> TCGA-02-0111-01A-01 2 0.0404 0.9632 0.000 0.988 0.000 0.000 0.012
#> TCGA-02-0326-01A-01 5 0.5246 0.5162 0.092 0.000 0.212 0.008 0.688
#> TCGA-02-0337-01A-01 2 0.3123 0.8401 0.000 0.828 0.000 0.012 0.160
#> TCGA-06-0122-01A-01 2 0.0880 0.9583 0.000 0.968 0.000 0.000 0.032
#> TCGA-06-0124-01A-01 2 0.0290 0.9637 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0130-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-06-0139-01A-01 2 0.0290 0.9651 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0143-01A-01 2 0.0880 0.9583 0.000 0.968 0.000 0.000 0.032
#> TCGA-06-0147-01A-01 2 0.0510 0.9650 0.000 0.984 0.000 0.000 0.016
#> TCGA-06-0149-01A-05 2 0.1408 0.9495 0.000 0.948 0.000 0.008 0.044
#> TCGA-06-0152-01A-02 3 0.2377 0.9009 0.000 0.000 0.872 0.000 0.128
#> TCGA-06-0154-01A-02 2 0.0880 0.9639 0.000 0.968 0.000 0.000 0.032
#> TCGA-06-0164-01A-01 2 0.0000 0.9645 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.0771 0.9618 0.000 0.976 0.000 0.004 0.020
#> TCGA-06-0176-01A-03 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-06-0184-01A-01 2 0.3182 0.8415 0.000 0.844 0.000 0.124 0.032
#> TCGA-06-0189-01A-05 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-06-0190-01A-01 2 0.0880 0.9635 0.000 0.968 0.000 0.000 0.032
#> TCGA-06-0194-01A-01 2 0.0000 0.9645 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0290 0.9651 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0210-01A-01 2 0.0404 0.9631 0.000 0.988 0.000 0.000 0.012
#> TCGA-06-0397-01A-01 2 0.0963 0.9630 0.000 0.964 0.000 0.000 0.036
#> TCGA-06-0409-01A-02 2 0.0609 0.9613 0.000 0.980 0.000 0.000 0.020
#> TCGA-06-0412-01A-01 2 0.1041 0.9570 0.000 0.964 0.004 0.000 0.032
#> TCGA-06-0644-01A-02 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-06-0645-01A-01 2 0.0794 0.9594 0.000 0.972 0.000 0.000 0.028
#> TCGA-08-0346-01A-01 2 0.0000 0.9645 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0352-01A-01 2 0.0794 0.9594 0.000 0.972 0.000 0.000 0.028
#> TCGA-08-0360-01A-01 2 0.0609 0.9613 0.000 0.980 0.000 0.000 0.020
#> TCGA-08-0390-01A-01 2 0.0000 0.9645 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0392-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-08-0509-01A-01 2 0.0609 0.9613 0.000 0.980 0.000 0.000 0.020
#> TCGA-08-0510-01A-01 2 0.0703 0.9612 0.000 0.976 0.000 0.000 0.024
#> TCGA-08-0512-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-08-0522-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-12-0619-01A-01 2 0.1043 0.9625 0.000 0.960 0.000 0.000 0.040
#> TCGA-12-0620-01A-01 2 0.1502 0.9349 0.000 0.940 0.004 0.000 0.056
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.2605 0.7912 0.864 0.000 0.000 0.000 0.108 0.028
#> TCGA-02-0010-01A-01 1 0.0146 0.8511 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0011-01B-01 5 0.3823 0.5181 0.436 0.000 0.000 0.000 0.564 0.000
#> TCGA-02-0014-01A-01 1 0.0146 0.8511 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0024-01B-01 1 0.0458 0.8515 0.984 0.000 0.000 0.000 0.016 0.000
#> TCGA-02-0026-01B-01 1 0.0146 0.8511 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0028-01A-01 1 0.0146 0.8511 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0046-01A-01 1 0.2445 0.7978 0.872 0.000 0.000 0.000 0.108 0.020
#> TCGA-02-0047-01A-01 5 0.5834 -0.4044 0.000 0.000 0.000 0.188 0.424 0.388
#> TCGA-02-0048-01A-01 1 0.0870 0.8467 0.972 0.000 0.012 0.000 0.012 0.004
#> TCGA-02-0060-01A-01 5 0.4715 0.6244 0.336 0.000 0.000 0.004 0.608 0.052
#> TCGA-02-0069-01A-01 1 0.0146 0.8511 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0074-01A-01 1 0.2301 0.8067 0.884 0.000 0.000 0.000 0.096 0.020
#> TCGA-02-0080-01A-01 5 0.3499 0.6570 0.320 0.000 0.000 0.000 0.680 0.000
#> TCGA-02-0084-01A-03 5 0.3376 0.5773 0.128 0.016 0.000 0.012 0.828 0.016
#> TCGA-02-0087-01A-01 5 0.3023 0.6390 0.212 0.000 0.000 0.004 0.784 0.000
#> TCGA-02-0104-01A-01 1 0.0146 0.8511 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0114-01A-01 1 0.0146 0.8511 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0281-01A-01 1 0.0146 0.8511 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0321-01A-01 1 0.5314 0.2915 0.544 0.000 0.000 0.000 0.336 0.120
#> TCGA-02-0325-01A-01 5 0.3565 0.6305 0.304 0.000 0.000 0.000 0.692 0.004
#> TCGA-02-0338-01A-01 1 0.0000 0.8513 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0146 0.8511 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0432-01A-02 5 0.3531 0.6529 0.328 0.000 0.000 0.000 0.672 0.000
#> TCGA-02-0439-01A-01 5 0.3559 0.4790 0.036 0.000 0.000 0.032 0.820 0.112
#> TCGA-02-0440-01A-01 1 0.2383 0.8047 0.880 0.000 0.000 0.000 0.096 0.024
#> TCGA-02-0446-01A-01 6 0.7315 0.4590 0.136 0.000 0.000 0.240 0.216 0.408
#> TCGA-06-0128-01A-01 5 0.3756 0.6356 0.352 0.000 0.000 0.004 0.644 0.000
#> TCGA-06-0129-01A-01 1 0.2003 0.7373 0.884 0.000 0.000 0.000 0.116 0.000
#> TCGA-06-0146-01A-01 5 0.3620 0.6346 0.352 0.000 0.000 0.000 0.648 0.000
#> TCGA-06-0156-01A-01 1 0.7551 -0.3927 0.328 0.000 0.000 0.172 0.204 0.296
#> TCGA-06-0166-01A-01 1 0.6499 0.0850 0.484 0.000 0.000 0.056 0.156 0.304
#> TCGA-06-0174-01A-01 1 0.2350 0.8043 0.880 0.000 0.000 0.000 0.100 0.020
#> TCGA-06-0177-01A-01 1 0.1967 0.8183 0.904 0.000 0.000 0.000 0.084 0.012
#> TCGA-06-0238-01A-02 5 0.4796 0.4580 0.396 0.000 0.000 0.020 0.560 0.024
#> TCGA-06-0241-01A-02 1 0.1753 0.8233 0.912 0.000 0.000 0.000 0.084 0.004
#> TCGA-06-0410-01A-01 1 0.0858 0.8487 0.968 0.000 0.000 0.000 0.028 0.004
#> TCGA-06-0413-01A-01 1 0.0458 0.8515 0.984 0.000 0.000 0.000 0.016 0.000
#> TCGA-06-0414-01A-01 1 0.2350 0.8045 0.880 0.000 0.000 0.000 0.100 0.020
#> TCGA-06-0646-01A-01 6 0.7689 0.5276 0.104 0.032 0.000 0.212 0.232 0.420
#> TCGA-06-0648-01A-01 1 0.1663 0.8146 0.912 0.000 0.000 0.000 0.088 0.000
#> TCGA-08-0245-01A-01 1 0.0405 0.8517 0.988 0.000 0.000 0.000 0.008 0.004
#> TCGA-08-0344-01A-01 1 0.0260 0.8493 0.992 0.000 0.000 0.000 0.008 0.000
#> TCGA-08-0347-01A-01 5 0.6074 -0.3428 0.020 0.000 0.000 0.148 0.448 0.384
#> TCGA-08-0348-01A-01 1 0.4892 0.0274 0.500 0.000 0.000 0.000 0.440 0.060
#> TCGA-08-0350-01A-01 5 0.3695 0.6073 0.376 0.000 0.000 0.000 0.624 0.000
#> TCGA-08-0353-01A-01 3 0.3065 0.7081 0.172 0.000 0.812 0.000 0.008 0.008
#> TCGA-08-0359-01A-01 5 0.5330 0.1360 0.020 0.000 0.000 0.108 0.628 0.244
#> TCGA-08-0385-01A-01 1 0.1267 0.8060 0.940 0.000 0.000 0.000 0.060 0.000
#> TCGA-08-0517-01A-01 1 0.0508 0.8511 0.984 0.000 0.000 0.000 0.012 0.004
#> TCGA-08-0524-01A-01 1 0.0146 0.8511 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-12-0616-01A-01 1 0.0458 0.8515 0.984 0.000 0.000 0.000 0.016 0.000
#> TCGA-12-0618-01A-01 1 0.0937 0.8442 0.960 0.000 0.000 0.000 0.040 0.000
#> TCGA-02-0089-01A-01 4 0.4191 0.2645 0.000 0.004 0.000 0.596 0.012 0.388
#> TCGA-02-0113-01A-01 4 0.4628 0.4124 0.000 0.000 0.268 0.668 0.012 0.052
#> TCGA-02-0115-01A-01 4 0.3979 0.3338 0.000 0.000 0.000 0.628 0.012 0.360
#> TCGA-02-0451-01A-01 4 0.3954 0.3389 0.000 0.000 0.000 0.636 0.012 0.352
#> TCGA-06-0132-01A-02 4 0.4155 0.3151 0.000 0.000 0.000 0.616 0.020 0.364
#> TCGA-06-0133-01A-02 4 0.0146 0.6542 0.000 0.000 0.000 0.996 0.004 0.000
#> TCGA-06-0138-01A-02 4 0.3240 0.5574 0.000 0.000 0.000 0.812 0.040 0.148
#> TCGA-06-0160-01A-01 5 0.5023 0.2895 0.012 0.000 0.000 0.356 0.576 0.056
#> TCGA-06-0162-01A-01 4 0.0146 0.6542 0.000 0.000 0.000 0.996 0.004 0.000
#> TCGA-06-0167-01A-01 5 0.5023 0.2895 0.012 0.000 0.000 0.356 0.576 0.056
#> TCGA-06-0171-01A-02 4 0.0937 0.6468 0.000 0.000 0.000 0.960 0.000 0.040
#> TCGA-06-0173-01A-01 4 0.4344 0.2817 0.000 0.000 0.000 0.612 0.032 0.356
#> TCGA-06-0179-01A-02 4 0.3883 0.3871 0.000 0.000 0.000 0.656 0.012 0.332
#> TCGA-06-0182-01A-01 4 0.4327 0.4088 0.000 0.000 0.284 0.676 0.012 0.028
#> TCGA-06-0185-01A-01 4 0.4071 0.4695 0.000 0.000 0.216 0.736 0.012 0.036
#> TCGA-06-0195-01B-01 4 0.1838 0.6293 0.000 0.000 0.000 0.916 0.068 0.016
#> TCGA-06-0208-01B-01 4 0.0291 0.6539 0.000 0.000 0.004 0.992 0.000 0.004
#> TCGA-06-0214-01A-02 4 0.4437 0.2114 0.000 0.000 0.000 0.576 0.032 0.392
#> TCGA-06-0219-01A-01 4 0.0508 0.6530 0.000 0.000 0.000 0.984 0.004 0.012
#> TCGA-06-0221-01A-01 4 0.4514 0.4092 0.040 0.000 0.000 0.680 0.264 0.016
#> TCGA-06-0237-01A-02 4 0.1257 0.6442 0.000 0.000 0.000 0.952 0.028 0.020
#> TCGA-06-0240-01A-02 4 0.3168 0.5890 0.000 0.000 0.000 0.828 0.116 0.056
#> TCGA-08-0349-01A-01 4 0.0603 0.6523 0.000 0.000 0.000 0.980 0.004 0.016
#> TCGA-08-0380-01A-01 4 0.2697 0.5697 0.000 0.000 0.000 0.812 0.000 0.188
#> TCGA-08-0386-01A-01 4 0.4914 0.4928 0.004 0.000 0.144 0.724 0.044 0.084
#> TCGA-08-0520-01A-01 4 0.1930 0.6297 0.000 0.000 0.000 0.916 0.048 0.036
#> TCGA-02-0007-01A-01 1 0.7568 -0.0539 0.380 0.000 0.200 0.316 0.036 0.068
#> TCGA-02-0009-01A-01 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0016-01A-01 3 0.1657 0.8717 0.000 0.000 0.928 0.000 0.056 0.016
#> TCGA-02-0021-01A-01 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0023-01B-01 3 0.4793 0.7839 0.000 0.000 0.712 0.020 0.136 0.132
#> TCGA-02-0027-01A-01 3 0.2367 0.8451 0.020 0.000 0.900 0.004 0.064 0.012
#> TCGA-02-0038-01A-01 4 0.6068 0.0377 0.000 0.008 0.124 0.464 0.016 0.388
#> TCGA-02-0043-01A-01 3 0.0891 0.8787 0.000 0.000 0.968 0.000 0.008 0.024
#> TCGA-02-0070-01A-01 3 0.3292 0.8195 0.000 0.024 0.836 0.000 0.032 0.108
#> TCGA-02-0102-01A-01 3 0.0806 0.8794 0.000 0.000 0.972 0.000 0.008 0.020
#> TCGA-02-0260-01A-03 3 0.3792 0.8171 0.000 0.000 0.780 0.000 0.112 0.108
#> TCGA-02-0269-01B-01 3 0.3792 0.8171 0.000 0.000 0.780 0.000 0.112 0.108
#> TCGA-02-0285-01A-01 3 0.3884 0.8079 0.000 0.004 0.760 0.000 0.052 0.184
#> TCGA-02-0289-01A-01 3 0.2201 0.8661 0.000 0.000 0.900 0.000 0.052 0.048
#> TCGA-02-0290-01A-01 3 0.4488 0.7929 0.000 0.000 0.708 0.000 0.128 0.164
#> TCGA-02-0317-01A-01 3 0.3876 0.8127 0.000 0.000 0.772 0.000 0.120 0.108
#> TCGA-02-0333-01A-02 3 0.3876 0.8127 0.000 0.000 0.772 0.000 0.120 0.108
#> TCGA-02-0422-01A-01 3 0.0405 0.8792 0.000 0.000 0.988 0.000 0.008 0.004
#> TCGA-02-0430-01A-01 3 0.0603 0.8802 0.000 0.000 0.980 0.000 0.004 0.016
#> TCGA-06-0125-01A-01 3 0.0146 0.8800 0.000 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0126-01A-01 3 0.0000 0.8799 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.0363 0.8805 0.000 0.000 0.988 0.000 0.000 0.012
#> TCGA-06-0145-01A-04 3 0.0820 0.8789 0.000 0.000 0.972 0.000 0.012 0.016
#> TCGA-06-0148-01A-01 3 0.4117 0.8156 0.000 0.000 0.748 0.000 0.112 0.140
#> TCGA-06-0187-01A-01 3 0.3294 0.8081 0.000 0.004 0.828 0.008 0.032 0.128
#> TCGA-06-0211-01B-01 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0402-01A-01 3 0.0603 0.8802 0.000 0.000 0.980 0.000 0.004 0.016
#> TCGA-08-0246-01A-01 3 0.7078 0.2545 0.000 0.220 0.480 0.032 0.044 0.224
#> TCGA-08-0354-01A-01 3 0.6020 0.7246 0.000 0.020 0.612 0.032 0.128 0.208
#> TCGA-08-0355-01A-01 3 0.4793 0.7831 0.000 0.000 0.712 0.020 0.136 0.132
#> TCGA-08-0357-01A-01 3 0.0405 0.8792 0.000 0.000 0.988 0.000 0.008 0.004
#> TCGA-08-0358-01A-01 3 0.3918 0.8104 0.000 0.000 0.768 0.000 0.124 0.108
#> TCGA-08-0375-01A-01 3 0.0508 0.8811 0.000 0.000 0.984 0.000 0.004 0.012
#> TCGA-08-0511-01A-01 3 0.0993 0.8768 0.000 0.000 0.964 0.000 0.012 0.024
#> TCGA-08-0514-01A-01 3 0.2309 0.8509 0.000 0.000 0.888 0.000 0.028 0.084
#> TCGA-08-0518-01A-01 3 0.1049 0.8786 0.000 0.000 0.960 0.000 0.008 0.032
#> TCGA-08-0529-01A-02 3 0.0725 0.8791 0.000 0.000 0.976 0.000 0.012 0.012
#> TCGA-08-0531-01A-01 3 0.0520 0.8799 0.000 0.000 0.984 0.000 0.008 0.008
#> TCGA-02-0057-01A-01 6 0.6311 0.4587 0.000 0.228 0.000 0.248 0.028 0.496
#> TCGA-02-0004-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-02-0006-01B-01 2 0.5314 -0.1147 0.000 0.484 0.000 0.056 0.020 0.440
#> TCGA-02-0025-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-02-0033-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-02-0034-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-02-0039-01A-01 2 0.2884 0.7015 0.000 0.824 0.000 0.004 0.008 0.164
#> TCGA-02-0051-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-02-0054-01A-01 2 0.4779 0.2949 0.000 0.568 0.000 0.040 0.008 0.384
#> TCGA-02-0055-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-02-0059-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-02-0064-01A-01 2 0.1531 0.7602 0.000 0.928 0.000 0.000 0.004 0.068
#> TCGA-02-0075-01A-01 2 0.2300 0.7807 0.000 0.856 0.000 0.000 0.000 0.144
#> TCGA-02-0079-01A-03 2 0.4525 0.5978 0.000 0.684 0.000 0.000 0.088 0.228
#> TCGA-02-0085-01A-01 6 0.6569 0.4973 0.000 0.212 0.000 0.276 0.044 0.468
#> TCGA-02-0086-01A-01 2 0.2402 0.7781 0.000 0.856 0.000 0.000 0.004 0.140
#> TCGA-02-0099-01A-01 2 0.4224 0.3896 0.000 0.512 0.000 0.004 0.008 0.476
#> TCGA-02-0106-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-02-0107-01A-01 2 0.2595 0.7068 0.000 0.836 0.000 0.000 0.004 0.160
#> TCGA-02-0111-01A-01 2 0.1349 0.7635 0.000 0.940 0.000 0.000 0.004 0.056
#> TCGA-02-0326-01A-01 5 0.5585 0.4175 0.076 0.000 0.140 0.004 0.672 0.108
#> TCGA-02-0337-01A-01 2 0.5238 0.2204 0.000 0.560 0.000 0.004 0.096 0.340
#> TCGA-06-0122-01A-01 2 0.3309 0.7031 0.000 0.800 0.004 0.000 0.024 0.172
#> TCGA-06-0124-01A-01 2 0.2491 0.7393 0.000 0.868 0.000 0.000 0.020 0.112
#> TCGA-06-0130-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-06-0139-01A-01 2 0.1863 0.7832 0.000 0.896 0.000 0.000 0.000 0.104
#> TCGA-06-0143-01A-01 2 0.3175 0.7093 0.000 0.808 0.000 0.000 0.028 0.164
#> TCGA-06-0147-01A-01 2 0.1444 0.7698 0.000 0.928 0.000 0.000 0.000 0.072
#> TCGA-06-0149-01A-05 2 0.4792 0.5324 0.000 0.644 0.000 0.020 0.044 0.292
#> TCGA-06-0152-01A-02 3 0.5272 0.7384 0.000 0.000 0.632 0.008 0.164 0.196
#> TCGA-06-0154-01A-02 2 0.3460 0.7528 0.000 0.760 0.000 0.000 0.020 0.220
#> TCGA-06-0164-01A-01 2 0.1204 0.7769 0.000 0.944 0.000 0.000 0.000 0.056
#> TCGA-06-0175-01A-01 2 0.3017 0.7167 0.000 0.816 0.000 0.000 0.020 0.164
#> TCGA-06-0176-01A-03 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-06-0184-01A-01 2 0.5241 0.3644 0.000 0.600 0.000 0.104 0.008 0.288
#> TCGA-06-0189-01A-05 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-06-0190-01A-01 2 0.3012 0.7702 0.000 0.796 0.000 0.000 0.008 0.196
#> TCGA-06-0194-01A-01 2 0.1204 0.7829 0.000 0.944 0.000 0.000 0.000 0.056
#> TCGA-06-0197-01A-02 2 0.2300 0.7787 0.000 0.856 0.000 0.000 0.000 0.144
#> TCGA-06-0210-01A-01 2 0.2432 0.7398 0.000 0.876 0.000 0.000 0.024 0.100
#> TCGA-06-0397-01A-01 2 0.3217 0.7649 0.000 0.768 0.000 0.000 0.008 0.224
#> TCGA-06-0409-01A-02 2 0.1644 0.7582 0.000 0.920 0.000 0.000 0.004 0.076
#> TCGA-06-0412-01A-01 2 0.2949 0.7196 0.000 0.832 0.000 0.000 0.028 0.140
#> TCGA-06-0644-01A-02 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-06-0645-01A-01 2 0.2572 0.7343 0.000 0.852 0.000 0.000 0.012 0.136
#> TCGA-08-0346-01A-01 2 0.1010 0.7701 0.000 0.960 0.000 0.000 0.004 0.036
#> TCGA-08-0352-01A-01 2 0.3403 0.6766 0.000 0.768 0.000 0.000 0.020 0.212
#> TCGA-08-0360-01A-01 2 0.1471 0.7607 0.000 0.932 0.000 0.000 0.004 0.064
#> TCGA-08-0390-01A-01 2 0.2278 0.7698 0.000 0.868 0.000 0.000 0.004 0.128
#> TCGA-08-0392-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-08-0509-01A-01 2 0.2320 0.7273 0.000 0.864 0.000 0.000 0.004 0.132
#> TCGA-08-0510-01A-01 2 0.3025 0.7145 0.000 0.820 0.000 0.000 0.024 0.156
#> TCGA-08-0512-01A-01 2 0.3133 0.7672 0.000 0.780 0.000 0.000 0.008 0.212
#> TCGA-08-0522-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-12-0619-01A-01 2 0.3161 0.7661 0.000 0.776 0.000 0.000 0.008 0.216
#> TCGA-12-0620-01A-01 2 0.4361 0.6012 0.000 0.716 0.004 0.000 0.076 0.204
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> SD:skmeans 168 9.69e-23 2
#> SD:skmeans 172 9.70e-57 3
#> SD:skmeans 166 1.98e-81 4
#> SD:skmeans 156 7.06e-84 5
#> SD:skmeans 138 5.12e-76 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "pam"]
# you can also extract it by
# res = res_list["SD:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.895 0.945 0.976 0.4121 0.582 0.582
#> 3 3 0.760 0.859 0.938 0.5522 0.765 0.599
#> 4 4 0.768 0.801 0.915 0.1523 0.854 0.616
#> 5 5 0.730 0.690 0.841 0.0404 0.946 0.806
#> 6 6 0.746 0.692 0.858 0.0145 0.974 0.894
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.6343 0.8093 0.840 0.160
#> TCGA-02-0047-01A-01 1 1.0000 0.0232 0.500 0.500
#> TCGA-02-0048-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.7139 0.7795 0.804 0.196
#> TCGA-02-0084-01A-03 2 0.0376 0.9837 0.004 0.996
#> TCGA-02-0087-01A-01 1 0.7674 0.7444 0.776 0.224
#> TCGA-02-0104-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.9427 0.5035 0.640 0.360
#> TCGA-02-0325-01A-01 1 0.7674 0.7444 0.776 0.224
#> TCGA-02-0338-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.5408 0.8540 0.876 0.124
#> TCGA-02-0440-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0446-01A-01 2 0.9881 0.1952 0.436 0.564
#> TCGA-06-0128-01A-01 1 0.6887 0.7803 0.816 0.184
#> TCGA-06-0129-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-06-0156-01A-01 2 0.8081 0.6549 0.248 0.752
#> TCGA-06-0166-01A-01 2 0.7674 0.6951 0.224 0.776
#> TCGA-06-0174-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-06-0238-01A-02 1 0.6712 0.8022 0.824 0.176
#> TCGA-06-0241-01A-02 1 0.0000 0.9439 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0648-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-08-0347-01A-01 2 0.9635 0.3433 0.388 0.612
#> TCGA-08-0348-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.7674 0.7444 0.776 0.224
#> TCGA-08-0353-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0359-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.7745 0.7405 0.772 0.228
#> TCGA-12-0618-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0115-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0138-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-06-0171-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0173-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0179-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0185-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.0000 0.9439 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.3431 0.9185 0.064 0.936
#> TCGA-06-0221-01A-01 1 0.5059 0.8640 0.888 0.112
#> TCGA-06-0237-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0240-01A-02 1 0.0000 0.9439 1.000 0.000
#> TCGA-08-0349-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0386-01A-01 2 0.1843 0.9591 0.028 0.972
#> TCGA-08-0520-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0007-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0009-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0016-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0021-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0023-01B-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0027-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0038-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0043-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0070-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0102-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0260-01A-03 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0269-01B-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0285-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0289-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0290-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0317-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0333-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0422-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0430-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0125-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0126-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0137-01A-03 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0145-01A-04 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0148-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0187-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0211-01B-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0402-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0246-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0357-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0358-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0375-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0511-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0514-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0529-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0531-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0057-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.1414 0.9675 0.020 0.980
#> TCGA-02-0337-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9876 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9876 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.9876 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.4062 0.781 0.836 0.000 0.164
#> TCGA-02-0047-01A-01 1 0.9004 0.211 0.488 0.136 0.376
#> TCGA-02-0048-01A-01 1 0.0237 0.923 0.996 0.000 0.004
#> TCGA-02-0060-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.4504 0.762 0.804 0.000 0.196
#> TCGA-02-0084-01A-03 3 0.0237 0.942 0.004 0.000 0.996
#> TCGA-02-0087-01A-01 1 0.4750 0.740 0.784 0.000 0.216
#> TCGA-02-0104-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.5926 0.508 0.644 0.000 0.356
#> TCGA-02-0325-01A-01 1 0.4750 0.740 0.784 0.000 0.216
#> TCGA-02-0338-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0439-01A-01 1 0.3340 0.834 0.880 0.000 0.120
#> TCGA-02-0440-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.9370 -0.104 0.420 0.412 0.168
#> TCGA-06-0128-01A-01 1 0.4452 0.750 0.808 0.000 0.192
#> TCGA-06-0129-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 3 0.6108 0.652 0.240 0.028 0.732
#> TCGA-06-0166-01A-01 3 0.5597 0.691 0.216 0.020 0.764
#> TCGA-06-0174-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.4235 0.782 0.824 0.000 0.176
#> TCGA-06-0241-01A-02 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.0237 0.942 0.000 0.004 0.996
#> TCGA-06-0648-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-08-0347-01A-01 3 0.6026 0.394 0.376 0.000 0.624
#> TCGA-08-0348-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-08-0350-01A-01 1 0.4750 0.740 0.784 0.000 0.216
#> TCGA-08-0353-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0359-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.4887 0.729 0.772 0.000 0.228
#> TCGA-12-0618-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-02-0089-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0113-01A-01 3 0.1163 0.925 0.000 0.028 0.972
#> TCGA-02-0115-01A-01 2 0.5835 0.572 0.000 0.660 0.340
#> TCGA-02-0451-01A-01 3 0.6192 0.173 0.000 0.420 0.580
#> TCGA-06-0132-01A-02 2 0.4452 0.790 0.000 0.808 0.192
#> TCGA-06-0133-01A-02 3 0.3816 0.785 0.000 0.148 0.852
#> TCGA-06-0138-01A-02 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-06-0162-01A-01 2 0.5058 0.733 0.000 0.756 0.244
#> TCGA-06-0167-01A-01 1 0.0000 0.925 1.000 0.000 0.000
#> TCGA-06-0171-01A-02 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0179-01A-02 2 0.4452 0.790 0.000 0.808 0.192
#> TCGA-06-0182-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.0237 0.923 0.996 0.000 0.004
#> TCGA-06-0208-01B-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 3 0.7300 0.506 0.064 0.272 0.664
#> TCGA-06-0221-01A-01 1 0.3267 0.839 0.884 0.000 0.116
#> TCGA-06-0237-01A-02 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 1 0.0237 0.923 0.996 0.000 0.004
#> TCGA-08-0349-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.4887 0.753 0.000 0.772 0.228
#> TCGA-08-0386-01A-01 3 0.1163 0.922 0.028 0.000 0.972
#> TCGA-08-0520-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0009-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0016-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0021-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0023-01B-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0027-01A-01 3 0.0892 0.932 0.000 0.020 0.980
#> TCGA-02-0038-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0043-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0070-01A-01 3 0.0237 0.942 0.000 0.004 0.996
#> TCGA-02-0102-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0260-01A-03 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0269-01B-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0285-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0289-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0290-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0317-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0333-01A-02 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0422-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0430-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0125-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0126-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0137-01A-03 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0145-01A-04 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0148-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0187-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0211-01B-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0402-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0246-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0354-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0355-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0357-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0358-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0375-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0511-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0514-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0518-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0529-01A-02 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-08-0531-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0057-01A-01 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.4452 0.790 0.000 0.808 0.192
#> TCGA-02-0025-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-02-0039-01A-01 2 0.0424 0.896 0.000 0.992 0.008
#> TCGA-02-0051-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-02-0054-01A-01 2 0.6299 0.204 0.000 0.524 0.476
#> TCGA-02-0055-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 2 0.5138 0.675 0.000 0.748 0.252
#> TCGA-02-0075-01A-01 2 0.3412 0.816 0.000 0.876 0.124
#> TCGA-02-0079-01A-03 3 0.1643 0.910 0.000 0.044 0.956
#> TCGA-02-0085-01A-01 2 0.6079 0.447 0.000 0.612 0.388
#> TCGA-02-0086-01A-01 2 0.4399 0.794 0.000 0.812 0.188
#> TCGA-02-0099-01A-01 2 0.4452 0.790 0.000 0.808 0.192
#> TCGA-02-0106-01A-01 3 0.5016 0.668 0.000 0.240 0.760
#> TCGA-02-0107-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-02-0326-01A-01 3 0.0747 0.931 0.016 0.000 0.984
#> TCGA-02-0337-01A-01 3 0.1529 0.915 0.000 0.040 0.960
#> TCGA-06-0122-01A-01 3 0.0237 0.942 0.000 0.004 0.996
#> TCGA-06-0124-01A-01 3 0.4654 0.710 0.000 0.208 0.792
#> TCGA-06-0130-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-06-0143-01A-01 3 0.1643 0.912 0.000 0.044 0.956
#> TCGA-06-0147-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 3 0.0237 0.942 0.000 0.004 0.996
#> TCGA-06-0152-01A-02 3 0.0000 0.944 0.000 0.000 1.000
#> TCGA-06-0154-01A-02 3 0.1411 0.918 0.000 0.036 0.964
#> TCGA-06-0164-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 3 0.0237 0.942 0.000 0.004 0.996
#> TCGA-06-0176-01A-03 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.4931 0.747 0.000 0.768 0.232
#> TCGA-06-0189-01A-05 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-06-0210-01A-01 3 0.6079 0.306 0.000 0.388 0.612
#> TCGA-06-0397-01A-01 2 0.1031 0.890 0.000 0.976 0.024
#> TCGA-06-0409-01A-02 2 0.4346 0.797 0.000 0.816 0.184
#> TCGA-06-0412-01A-01 3 0.0237 0.942 0.000 0.004 0.996
#> TCGA-06-0644-01A-02 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-06-0645-01A-01 3 0.4702 0.698 0.000 0.212 0.788
#> TCGA-08-0346-01A-01 2 0.0892 0.893 0.000 0.980 0.020
#> TCGA-08-0352-01A-01 3 0.0237 0.942 0.000 0.004 0.996
#> TCGA-08-0360-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.1031 0.890 0.000 0.976 0.024
#> TCGA-08-0392-01A-01 2 0.1031 0.890 0.000 0.976 0.024
#> TCGA-08-0509-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 3 0.5650 0.502 0.000 0.312 0.688
#> TCGA-08-0512-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.898 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 3 0.6192 0.282 0.000 0.420 0.580
#> TCGA-12-0620-01A-01 3 0.0747 0.934 0.000 0.016 0.984
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 4 0.3801 0.705 0.220 0.000 0.000 0.780
#> TCGA-02-0010-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0336 0.877 0.992 0.000 0.000 0.008
#> TCGA-02-0014-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.3356 0.727 0.824 0.000 0.176 0.000
#> TCGA-02-0047-01A-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-02-0048-01A-01 4 0.4008 0.672 0.244 0.000 0.000 0.756
#> TCGA-02-0060-01A-01 4 0.3873 0.695 0.228 0.000 0.000 0.772
#> TCGA-02-0069-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.3528 0.719 0.808 0.000 0.192 0.000
#> TCGA-02-0084-01A-03 3 0.3569 0.738 0.000 0.000 0.804 0.196
#> TCGA-02-0087-01A-01 1 0.6683 0.530 0.620 0.000 0.204 0.176
#> TCGA-02-0104-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.4697 0.471 0.644 0.000 0.356 0.000
#> TCGA-02-0325-01A-01 1 0.3649 0.708 0.796 0.000 0.204 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0439-01A-01 1 0.3649 0.722 0.796 0.000 0.000 0.204
#> TCGA-02-0440-01A-01 1 0.0336 0.877 0.992 0.000 0.000 0.008
#> TCGA-02-0446-01A-01 4 0.3569 0.730 0.196 0.000 0.000 0.804
#> TCGA-06-0128-01A-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0129-01A-01 1 0.0921 0.865 0.972 0.000 0.000 0.028
#> TCGA-06-0146-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-06-0156-01A-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0166-01A-01 4 0.3569 0.730 0.196 0.000 0.000 0.804
#> TCGA-06-0174-01A-01 1 0.0336 0.877 0.992 0.000 0.000 0.008
#> TCGA-06-0177-01A-01 1 0.0188 0.878 0.996 0.000 0.004 0.000
#> TCGA-06-0238-01A-02 1 0.3649 0.722 0.796 0.000 0.000 0.204
#> TCGA-06-0241-01A-02 1 0.4830 0.321 0.608 0.000 0.000 0.392
#> TCGA-06-0410-01A-01 4 0.4431 0.459 0.304 0.000 0.000 0.696
#> TCGA-06-0413-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.2345 0.813 0.900 0.000 0.000 0.100
#> TCGA-06-0646-01A-01 3 0.2973 0.797 0.000 0.000 0.856 0.144
#> TCGA-06-0648-01A-01 1 0.0188 0.878 0.996 0.000 0.004 0.000
#> TCGA-08-0245-01A-01 1 0.3942 0.648 0.764 0.000 0.000 0.236
#> TCGA-08-0344-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 4 0.6854 0.517 0.196 0.000 0.204 0.600
#> TCGA-08-0348-01A-01 1 0.0336 0.877 0.992 0.000 0.000 0.008
#> TCGA-08-0350-01A-01 1 0.3649 0.708 0.796 0.000 0.204 0.000
#> TCGA-08-0353-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.4855 0.270 0.600 0.000 0.000 0.400
#> TCGA-08-0385-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.1118 0.860 0.964 0.000 0.000 0.036
#> TCGA-08-0524-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.6005 0.170 0.500 0.000 0.040 0.460
#> TCGA-12-0618-01A-01 1 0.0000 0.879 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 4 0.0188 0.893 0.000 0.000 0.004 0.996
#> TCGA-02-0113-01A-01 4 0.0469 0.887 0.000 0.000 0.012 0.988
#> TCGA-02-0115-01A-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-02-0451-01A-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0132-01A-02 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0133-01A-02 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.4134 0.663 0.740 0.000 0.000 0.260
#> TCGA-06-0162-01A-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.4855 0.425 0.600 0.000 0.000 0.400
#> TCGA-06-0171-01A-02 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0179-01A-02 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 4 0.4776 0.377 0.000 0.000 0.376 0.624
#> TCGA-06-0185-01A-01 4 0.4843 0.328 0.000 0.000 0.396 0.604
#> TCGA-06-0195-01B-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0208-01B-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-08-0349-01A-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 4 0.4331 0.561 0.000 0.288 0.000 0.712
#> TCGA-08-0386-01A-01 3 0.4193 0.636 0.000 0.000 0.732 0.268
#> TCGA-08-0520-01A-01 4 0.0000 0.895 0.000 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.0188 0.911 0.000 0.000 0.996 0.004
#> TCGA-02-0009-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0016-01A-01 3 0.4843 0.370 0.000 0.000 0.604 0.396
#> TCGA-02-0021-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0027-01A-01 3 0.3356 0.762 0.000 0.000 0.824 0.176
#> TCGA-02-0038-01A-01 3 0.3123 0.770 0.000 0.000 0.844 0.156
#> TCGA-02-0043-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0126-01A-01 3 0.3610 0.733 0.000 0.000 0.800 0.200
#> TCGA-06-0137-01A-03 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0354-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0357-01A-01 3 0.3610 0.733 0.000 0.000 0.800 0.200
#> TCGA-08-0358-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0375-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-02-0057-01A-01 3 0.4830 0.376 0.000 0.000 0.608 0.392
#> TCGA-02-0004-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.4855 0.407 0.000 0.600 0.400 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.1118 0.882 0.000 0.964 0.036 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 3 0.5000 -0.143 0.000 0.500 0.500 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.4730 0.442 0.000 0.636 0.364 0.000
#> TCGA-02-0075-01A-01 2 0.2589 0.802 0.000 0.884 0.116 0.000
#> TCGA-02-0079-01A-03 3 0.2408 0.828 0.000 0.104 0.896 0.000
#> TCGA-02-0085-01A-01 4 0.2271 0.840 0.000 0.076 0.008 0.916
#> TCGA-02-0086-01A-01 2 0.4817 0.434 0.000 0.612 0.388 0.000
#> TCGA-02-0099-01A-01 2 0.5244 0.423 0.000 0.600 0.388 0.012
#> TCGA-02-0106-01A-01 3 0.4941 0.252 0.000 0.436 0.564 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0707 0.900 0.020 0.000 0.980 0.000
#> TCGA-02-0337-01A-01 3 0.4990 0.464 0.000 0.008 0.640 0.352
#> TCGA-06-0122-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0124-01A-01 3 0.1118 0.888 0.000 0.036 0.964 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0154-01A-02 3 0.1118 0.888 0.000 0.036 0.964 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.6681 0.511 0.000 0.588 0.292 0.120
#> TCGA-06-0189-01A-05 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-06-0210-01A-01 3 0.4072 0.599 0.000 0.252 0.748 0.000
#> TCGA-06-0397-01A-01 2 0.0707 0.891 0.000 0.980 0.020 0.000
#> TCGA-06-0409-01A-02 2 0.4761 0.468 0.000 0.628 0.372 0.000
#> TCGA-06-0412-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 3 0.1211 0.884 0.000 0.040 0.960 0.000
#> TCGA-08-0346-01A-01 2 0.1716 0.861 0.000 0.936 0.064 0.000
#> TCGA-08-0352-01A-01 3 0.0000 0.913 0.000 0.000 1.000 0.000
#> TCGA-08-0360-01A-01 2 0.0469 0.897 0.000 0.988 0.012 0.000
#> TCGA-08-0390-01A-01 2 0.3444 0.713 0.000 0.816 0.000 0.184
#> TCGA-08-0392-01A-01 2 0.0188 0.901 0.000 0.996 0.004 0.000
#> TCGA-08-0509-01A-01 2 0.0469 0.897 0.000 0.988 0.012 0.000
#> TCGA-08-0510-01A-01 3 0.4304 0.534 0.000 0.284 0.716 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.902 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 3 0.4967 0.205 0.000 0.452 0.548 0.000
#> TCGA-12-0620-01A-01 3 0.0469 0.905 0.000 0.012 0.988 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 4 0.5831 0.39371 0.292 0.000 0.000 0.580 0.128
#> TCGA-02-0010-01A-01 5 0.3003 0.47993 0.188 0.000 0.000 0.000 0.812
#> TCGA-02-0011-01B-01 5 0.3039 0.25676 0.192 0.000 0.000 0.000 0.808
#> TCGA-02-0014-01A-01 1 0.3561 0.66705 0.740 0.000 0.000 0.000 0.260
#> TCGA-02-0024-01B-01 1 0.3561 0.66705 0.740 0.000 0.000 0.000 0.260
#> TCGA-02-0026-01B-01 5 0.4227 0.18040 0.420 0.000 0.000 0.000 0.580
#> TCGA-02-0028-01A-01 1 0.3895 0.59638 0.680 0.000 0.000 0.000 0.320
#> TCGA-02-0046-01A-01 1 0.5352 0.62599 0.536 0.000 0.056 0.000 0.408
#> TCGA-02-0047-01A-01 4 0.2648 0.71977 0.000 0.000 0.000 0.848 0.152
#> TCGA-02-0048-01A-01 4 0.4084 0.51052 0.328 0.000 0.000 0.668 0.004
#> TCGA-02-0060-01A-01 4 0.4430 0.64385 0.076 0.000 0.000 0.752 0.172
#> TCGA-02-0069-01A-01 5 0.3039 0.47830 0.192 0.000 0.000 0.000 0.808
#> TCGA-02-0074-01A-01 1 0.4283 0.71054 0.544 0.000 0.000 0.000 0.456
#> TCGA-02-0080-01A-01 5 0.0000 0.49219 0.000 0.000 0.000 0.000 1.000
#> TCGA-02-0084-01A-03 5 0.6048 0.26200 0.148 0.000 0.228 0.012 0.612
#> TCGA-02-0087-01A-01 5 0.1197 0.47296 0.000 0.000 0.000 0.048 0.952
#> TCGA-02-0104-01A-01 1 0.4273 0.31330 0.552 0.000 0.000 0.000 0.448
#> TCGA-02-0114-01A-01 1 0.4287 0.27743 0.540 0.000 0.000 0.000 0.460
#> TCGA-02-0281-01A-01 5 0.4294 0.08285 0.468 0.000 0.000 0.000 0.532
#> TCGA-02-0321-01A-01 3 0.6455 -0.00556 0.264 0.000 0.500 0.000 0.236
#> TCGA-02-0325-01A-01 5 0.3661 0.02893 0.276 0.000 0.000 0.000 0.724
#> TCGA-02-0338-01A-01 1 0.3561 0.66705 0.740 0.000 0.000 0.000 0.260
#> TCGA-02-0339-01A-01 5 0.4249 0.18891 0.432 0.000 0.000 0.000 0.568
#> TCGA-02-0432-01A-02 5 0.0000 0.49219 0.000 0.000 0.000 0.000 1.000
#> TCGA-02-0439-01A-01 5 0.6650 -0.16081 0.276 0.000 0.000 0.276 0.448
#> TCGA-02-0440-01A-01 1 0.4273 0.71573 0.552 0.000 0.000 0.000 0.448
#> TCGA-02-0446-01A-01 4 0.3639 0.69723 0.044 0.000 0.000 0.812 0.144
#> TCGA-06-0128-01A-01 4 0.3913 0.53618 0.000 0.000 0.000 0.676 0.324
#> TCGA-06-0129-01A-01 5 0.3760 0.47380 0.188 0.000 0.000 0.028 0.784
#> TCGA-06-0146-01A-01 5 0.3003 0.47993 0.188 0.000 0.000 0.000 0.812
#> TCGA-06-0156-01A-01 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0166-01A-01 4 0.1197 0.79033 0.048 0.000 0.000 0.952 0.000
#> TCGA-06-0174-01A-01 1 0.4273 0.71573 0.552 0.000 0.000 0.000 0.448
#> TCGA-06-0177-01A-01 1 0.4294 0.69365 0.532 0.000 0.000 0.000 0.468
#> TCGA-06-0238-01A-02 5 0.6650 -0.16621 0.280 0.000 0.000 0.272 0.448
#> TCGA-06-0241-01A-02 1 0.6477 0.33962 0.496 0.000 0.000 0.256 0.248
#> TCGA-06-0410-01A-01 4 0.5013 0.47941 0.204 0.000 0.000 0.696 0.100
#> TCGA-06-0413-01A-01 1 0.3561 0.66705 0.740 0.000 0.000 0.000 0.260
#> TCGA-06-0414-01A-01 1 0.4273 0.71573 0.552 0.000 0.000 0.000 0.448
#> TCGA-06-0646-01A-01 3 0.2719 0.78242 0.004 0.000 0.852 0.144 0.000
#> TCGA-06-0648-01A-01 1 0.4273 0.71573 0.552 0.000 0.000 0.000 0.448
#> TCGA-08-0245-01A-01 1 0.5176 0.67719 0.572 0.000 0.000 0.048 0.380
#> TCGA-08-0344-01A-01 1 0.4060 0.57230 0.640 0.000 0.000 0.000 0.360
#> TCGA-08-0347-01A-01 4 0.6954 0.37524 0.048 0.000 0.240 0.544 0.168
#> TCGA-08-0348-01A-01 1 0.4273 0.71573 0.552 0.000 0.000 0.000 0.448
#> TCGA-08-0350-01A-01 5 0.0000 0.49219 0.000 0.000 0.000 0.000 1.000
#> TCGA-08-0353-01A-01 3 0.0290 0.89011 0.008 0.000 0.992 0.000 0.000
#> TCGA-08-0359-01A-01 4 0.5578 0.42894 0.112 0.000 0.000 0.616 0.272
#> TCGA-08-0385-01A-01 5 0.3857 -0.05552 0.312 0.000 0.000 0.000 0.688
#> TCGA-08-0517-01A-01 1 0.4150 0.71734 0.612 0.000 0.000 0.000 0.388
#> TCGA-08-0524-01A-01 1 0.3561 0.66705 0.740 0.000 0.000 0.000 0.260
#> TCGA-12-0616-01A-01 4 0.6069 0.47198 0.200 0.000 0.048 0.652 0.100
#> TCGA-12-0618-01A-01 1 0.4273 0.71573 0.552 0.000 0.000 0.000 0.448
#> TCGA-02-0089-01A-01 4 0.2605 0.72013 0.148 0.000 0.000 0.852 0.000
#> TCGA-02-0113-01A-01 4 0.0404 0.80616 0.000 0.000 0.012 0.988 0.000
#> TCGA-02-0115-01A-01 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0451-01A-01 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0132-01A-02 4 0.0290 0.80935 0.008 0.000 0.000 0.992 0.000
#> TCGA-06-0133-01A-02 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0138-01A-02 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0160-01A-01 4 0.6443 -0.05287 0.376 0.000 0.000 0.444 0.180
#> TCGA-06-0162-01A-01 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0167-01A-01 4 0.6367 0.00267 0.372 0.000 0.000 0.460 0.168
#> TCGA-06-0171-01A-02 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0173-01A-01 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0179-01A-02 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0182-01A-01 4 0.4114 0.39366 0.000 0.000 0.376 0.624 0.000
#> TCGA-06-0185-01A-01 4 0.4171 0.34300 0.000 0.000 0.396 0.604 0.000
#> TCGA-06-0195-01B-01 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0208-01B-01 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0214-01A-02 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0219-01A-01 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0221-01A-01 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0237-01A-02 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0240-01A-02 4 0.2020 0.77048 0.100 0.000 0.000 0.900 0.000
#> TCGA-08-0349-01A-01 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-08-0380-01A-01 4 0.3730 0.51576 0.000 0.288 0.000 0.712 0.000
#> TCGA-08-0386-01A-01 3 0.4712 0.57625 0.048 0.000 0.684 0.268 0.000
#> TCGA-08-0520-01A-01 4 0.0000 0.81219 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0007-01A-01 3 0.0162 0.89207 0.000 0.000 0.996 0.004 0.000
#> TCGA-02-0009-01A-01 3 0.0290 0.89170 0.008 0.000 0.992 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.4415 0.39051 0.008 0.000 0.604 0.388 0.000
#> TCGA-02-0021-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0027-01A-01 3 0.2891 0.74838 0.000 0.000 0.824 0.176 0.000
#> TCGA-02-0038-01A-01 3 0.2690 0.75766 0.000 0.000 0.844 0.156 0.000
#> TCGA-02-0043-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.0290 0.89170 0.008 0.000 0.992 0.000 0.000
#> TCGA-02-0269-01B-01 3 0.0290 0.89170 0.008 0.000 0.992 0.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0289-01A-01 3 0.0290 0.89170 0.008 0.000 0.992 0.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0317-01A-01 3 0.0290 0.89170 0.008 0.000 0.992 0.000 0.000
#> TCGA-02-0333-01A-02 3 0.0290 0.89170 0.008 0.000 0.992 0.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.3109 0.71867 0.000 0.000 0.800 0.200 0.000
#> TCGA-06-0137-01A-03 3 0.0162 0.89259 0.004 0.000 0.996 0.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0354-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0357-01A-01 3 0.3109 0.71867 0.000 0.000 0.800 0.200 0.000
#> TCGA-08-0358-01A-01 3 0.0290 0.89170 0.008 0.000 0.992 0.000 0.000
#> TCGA-08-0375-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0518-01A-01 3 0.0162 0.89259 0.004 0.000 0.996 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.0290 0.89170 0.008 0.000 0.992 0.000 0.000
#> TCGA-02-0057-01A-01 3 0.5554 0.43646 0.092 0.000 0.592 0.316 0.000
#> TCGA-02-0004-01A-01 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.5832 0.62099 0.152 0.600 0.248 0.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0880 0.86816 0.032 0.968 0.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.2806 0.84281 0.152 0.844 0.004 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0054-01A-01 3 0.4307 -0.13407 0.000 0.500 0.500 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.5810 0.59836 0.152 0.604 0.244 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.2230 0.77557 0.000 0.884 0.116 0.000 0.000
#> TCGA-02-0079-01A-03 3 0.3495 0.77046 0.152 0.032 0.816 0.000 0.000
#> TCGA-02-0085-01A-01 4 0.4473 0.65493 0.148 0.076 0.008 0.768 0.000
#> TCGA-02-0086-01A-01 2 0.5726 0.62856 0.140 0.612 0.248 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.6107 0.62289 0.144 0.600 0.244 0.012 0.000
#> TCGA-02-0106-01A-01 3 0.4256 0.31723 0.000 0.436 0.564 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.2648 0.84393 0.152 0.848 0.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.2648 0.84393 0.152 0.848 0.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0794 0.88021 0.028 0.000 0.972 0.000 0.000
#> TCGA-02-0337-01A-01 3 0.7968 0.27439 0.152 0.008 0.472 0.244 0.124
#> TCGA-06-0122-01A-01 3 0.0162 0.89222 0.004 0.000 0.996 0.000 0.000
#> TCGA-06-0124-01A-01 3 0.2850 0.81643 0.092 0.036 0.872 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.2648 0.84393 0.152 0.848 0.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.2605 0.79531 0.148 0.000 0.852 0.000 0.000
#> TCGA-06-0147-01A-01 2 0.2648 0.84393 0.152 0.848 0.000 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0154-01A-02 3 0.1124 0.87168 0.004 0.036 0.960 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.2648 0.84393 0.152 0.848 0.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.6849 0.63422 0.152 0.588 0.188 0.072 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0162 0.87017 0.004 0.996 0.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.2648 0.84393 0.152 0.848 0.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0210-01A-01 3 0.3508 0.60534 0.000 0.252 0.748 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0609 0.86206 0.000 0.980 0.020 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.5764 0.63605 0.152 0.612 0.236 0.000 0.000
#> TCGA-06-0412-01A-01 3 0.0000 0.89331 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0645-01A-01 3 0.3608 0.76113 0.148 0.040 0.812 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.1638 0.84652 0.004 0.932 0.064 0.000 0.000
#> TCGA-08-0352-01A-01 3 0.2605 0.79531 0.148 0.000 0.852 0.000 0.000
#> TCGA-08-0360-01A-01 2 0.2929 0.84125 0.152 0.840 0.008 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.3732 0.72667 0.032 0.792 0.000 0.176 0.000
#> TCGA-08-0392-01A-01 2 0.0162 0.86911 0.000 0.996 0.004 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.2806 0.84281 0.152 0.844 0.004 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.3861 0.53720 0.004 0.284 0.712 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.87034 0.000 1.000 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 3 0.4278 0.27286 0.000 0.452 0.548 0.000 0.000
#> TCGA-12-0620-01A-01 3 0.0404 0.88767 0.000 0.012 0.988 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 6 0.3823 0.3449 0.436 0.000 0.000 0.000 0.000 0.564
#> TCGA-02-0010-01A-01 5 0.2416 0.6629 0.156 0.000 0.000 0.000 0.844 0.000
#> TCGA-02-0011-01B-01 1 0.3828 -0.2691 0.560 0.000 0.000 0.000 0.440 0.000
#> TCGA-02-0014-01A-01 1 0.2823 0.6305 0.796 0.000 0.000 0.000 0.204 0.000
#> TCGA-02-0024-01B-01 1 0.2793 0.6320 0.800 0.000 0.000 0.000 0.200 0.000
#> TCGA-02-0026-01B-01 5 0.3867 -0.0226 0.488 0.000 0.000 0.000 0.512 0.000
#> TCGA-02-0028-01A-01 1 0.3221 0.5775 0.736 0.000 0.000 0.000 0.264 0.000
#> TCGA-02-0046-01A-01 1 0.1075 0.6471 0.952 0.000 0.048 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 6 0.2562 0.6850 0.172 0.000 0.000 0.000 0.000 0.828
#> TCGA-02-0048-01A-01 6 0.3684 0.4586 0.332 0.000 0.000 0.004 0.000 0.664
#> TCGA-02-0060-01A-01 6 0.3244 0.6016 0.268 0.000 0.000 0.000 0.000 0.732
#> TCGA-02-0069-01A-01 5 0.2491 0.6592 0.164 0.000 0.000 0.000 0.836 0.000
#> TCGA-02-0074-01A-01 1 0.0363 0.6882 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-02-0080-01A-01 5 0.3634 0.6328 0.356 0.000 0.000 0.000 0.644 0.000
#> TCGA-02-0084-01A-03 5 0.3685 0.3198 0.080 0.000 0.120 0.000 0.796 0.004
#> TCGA-02-0087-01A-01 5 0.4285 0.6155 0.320 0.000 0.000 0.000 0.644 0.036
#> TCGA-02-0104-01A-01 1 0.3756 0.3329 0.600 0.000 0.000 0.000 0.400 0.000
#> TCGA-02-0114-01A-01 1 0.3774 0.3074 0.592 0.000 0.000 0.000 0.408 0.000
#> TCGA-02-0281-01A-01 1 0.3862 0.0764 0.524 0.000 0.000 0.000 0.476 0.000
#> TCGA-02-0321-01A-01 3 0.3864 0.1085 0.480 0.000 0.520 0.000 0.000 0.000
#> TCGA-02-0325-01A-01 1 0.3330 0.2431 0.716 0.000 0.000 0.000 0.284 0.000
#> TCGA-02-0338-01A-01 1 0.2793 0.6320 0.800 0.000 0.000 0.000 0.200 0.000
#> TCGA-02-0339-01A-01 5 0.3866 -0.0387 0.484 0.000 0.000 0.000 0.516 0.000
#> TCGA-02-0432-01A-02 5 0.3634 0.6328 0.356 0.000 0.000 0.000 0.644 0.000
#> TCGA-02-0439-01A-01 1 0.3330 0.3478 0.716 0.000 0.000 0.000 0.000 0.284
#> TCGA-02-0440-01A-01 1 0.0000 0.6923 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 6 0.2793 0.6687 0.200 0.000 0.000 0.000 0.000 0.800
#> TCGA-06-0128-01A-01 6 0.4779 0.3122 0.060 0.000 0.000 0.000 0.368 0.572
#> TCGA-06-0129-01A-01 5 0.2826 0.6532 0.128 0.000 0.000 0.000 0.844 0.028
#> TCGA-06-0146-01A-01 5 0.2416 0.6629 0.156 0.000 0.000 0.000 0.844 0.000
#> TCGA-06-0156-01A-01 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0166-01A-01 6 0.1075 0.7787 0.048 0.000 0.000 0.000 0.000 0.952
#> TCGA-06-0174-01A-01 1 0.0000 0.6923 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0547 0.6833 0.980 0.000 0.000 0.000 0.020 0.000
#> TCGA-06-0238-01A-02 1 0.3288 0.3577 0.724 0.000 0.000 0.000 0.000 0.276
#> TCGA-06-0241-01A-02 1 0.3050 0.4680 0.764 0.000 0.000 0.000 0.000 0.236
#> TCGA-06-0410-01A-01 6 0.3446 0.4584 0.308 0.000 0.000 0.000 0.000 0.692
#> TCGA-06-0413-01A-01 1 0.2793 0.6320 0.800 0.000 0.000 0.000 0.200 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.6923 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.2442 0.7794 0.000 0.000 0.852 0.000 0.004 0.144
#> TCGA-06-0648-01A-01 1 0.0000 0.6923 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.1863 0.6745 0.920 0.000 0.000 0.000 0.036 0.044
#> TCGA-08-0344-01A-01 1 0.3288 0.5688 0.724 0.000 0.000 0.000 0.276 0.000
#> TCGA-08-0347-01A-01 6 0.5703 0.2833 0.236 0.000 0.240 0.000 0.000 0.524
#> TCGA-08-0348-01A-01 1 0.0000 0.6923 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-08-0350-01A-01 5 0.3634 0.6328 0.356 0.000 0.000 0.000 0.644 0.000
#> TCGA-08-0353-01A-01 3 0.0260 0.8793 0.008 0.000 0.992 0.000 0.000 0.000
#> TCGA-08-0359-01A-01 6 0.3706 0.4447 0.380 0.000 0.000 0.000 0.000 0.620
#> TCGA-08-0385-01A-01 1 0.3390 0.2957 0.704 0.000 0.000 0.000 0.296 0.000
#> TCGA-08-0517-01A-01 1 0.1444 0.6871 0.928 0.000 0.000 0.000 0.072 0.000
#> TCGA-08-0524-01A-01 1 0.2793 0.6320 0.800 0.000 0.000 0.000 0.200 0.000
#> TCGA-12-0616-01A-01 6 0.4313 0.4744 0.284 0.000 0.048 0.000 0.000 0.668
#> TCGA-12-0618-01A-01 1 0.0000 0.6923 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 6 0.2821 0.6600 0.000 0.000 0.000 0.016 0.152 0.832
#> TCGA-02-0113-01A-01 6 0.0363 0.7973 0.000 0.000 0.012 0.000 0.000 0.988
#> TCGA-02-0115-01A-01 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-02-0451-01A-01 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0132-01A-02 6 0.0260 0.8017 0.000 0.000 0.000 0.000 0.008 0.992
#> TCGA-06-0133-01A-02 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 4 0.1714 0.8973 0.092 0.000 0.000 0.908 0.000 0.000
#> TCGA-06-0162-01A-01 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 4 0.1714 0.8973 0.092 0.000 0.000 0.908 0.000 0.000
#> TCGA-06-0171-01A-02 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0179-01A-02 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 6 0.3695 0.3074 0.000 0.000 0.376 0.000 0.000 0.624
#> TCGA-06-0185-01A-01 6 0.3747 0.2835 0.000 0.000 0.396 0.000 0.000 0.604
#> TCGA-06-0195-01B-01 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0208-01B-01 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.1714 0.8059 0.000 0.000 0.000 0.908 0.000 0.092
#> TCGA-08-0349-01A-01 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 6 0.3351 0.4543 0.000 0.288 0.000 0.000 0.000 0.712
#> TCGA-08-0386-01A-01 3 0.4233 0.5803 0.048 0.000 0.684 0.000 0.000 0.268
#> TCGA-08-0520-01A-01 6 0.0000 0.8058 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.0146 0.8810 0.000 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0009-01A-01 3 0.1444 0.8600 0.000 0.000 0.928 0.072 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.4795 0.4708 0.000 0.000 0.604 0.072 0.000 0.324
#> TCGA-02-0021-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0027-01A-01 3 0.2597 0.7479 0.000 0.000 0.824 0.000 0.000 0.176
#> TCGA-02-0038-01A-01 3 0.2416 0.7442 0.000 0.000 0.844 0.000 0.000 0.156
#> TCGA-02-0043-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.1444 0.8600 0.000 0.000 0.928 0.072 0.000 0.000
#> TCGA-02-0269-01B-01 3 0.1444 0.8600 0.000 0.000 0.928 0.072 0.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0289-01A-01 3 0.1444 0.8600 0.000 0.000 0.928 0.072 0.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0317-01A-01 3 0.1444 0.8600 0.000 0.000 0.928 0.072 0.000 0.000
#> TCGA-02-0333-01A-02 3 0.1444 0.8600 0.000 0.000 0.928 0.072 0.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.2793 0.7189 0.000 0.000 0.800 0.000 0.000 0.200
#> TCGA-06-0137-01A-03 3 0.1327 0.8632 0.000 0.000 0.936 0.064 0.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0354-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0357-01A-01 3 0.2793 0.7189 0.000 0.000 0.800 0.000 0.000 0.200
#> TCGA-08-0358-01A-01 3 0.1444 0.8600 0.000 0.000 0.928 0.072 0.000 0.000
#> TCGA-08-0375-01A-01 3 0.0146 0.8814 0.000 0.000 0.996 0.004 0.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0518-01A-01 3 0.1007 0.8702 0.000 0.000 0.956 0.044 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.1444 0.8600 0.000 0.000 0.928 0.072 0.000 0.000
#> TCGA-02-0057-01A-01 3 0.5264 0.4432 0.000 0.000 0.588 0.008 0.100 0.304
#> TCGA-02-0004-01A-01 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.5657 0.5697 0.000 0.596 0.228 0.020 0.156 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.1010 0.8241 0.000 0.960 0.000 0.004 0.036 0.000
#> TCGA-02-0039-01A-01 2 0.2945 0.7933 0.000 0.824 0.000 0.020 0.156 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.3869 0.1422 0.000 0.500 0.500 0.000 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.5678 0.5165 0.000 0.592 0.232 0.020 0.156 0.000
#> TCGA-02-0075-01A-01 2 0.2003 0.7154 0.000 0.884 0.116 0.000 0.000 0.000
#> TCGA-02-0079-01A-03 3 0.3550 0.7350 0.000 0.024 0.800 0.020 0.156 0.000
#> TCGA-02-0085-01A-01 6 0.4488 0.5683 0.000 0.076 0.008 0.016 0.152 0.748
#> TCGA-02-0086-01A-01 2 0.5496 0.5734 0.000 0.608 0.236 0.016 0.140 0.000
#> TCGA-02-0099-01A-01 2 0.5846 0.5679 0.000 0.596 0.228 0.016 0.148 0.012
#> TCGA-02-0106-01A-01 3 0.3823 0.3361 0.000 0.436 0.564 0.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.2945 0.7933 0.000 0.824 0.000 0.020 0.156 0.000
#> TCGA-02-0111-01A-01 2 0.2945 0.7933 0.000 0.824 0.000 0.020 0.156 0.000
#> TCGA-02-0326-01A-01 3 0.1701 0.8558 0.008 0.000 0.920 0.072 0.000 0.000
#> TCGA-02-0337-01A-01 3 0.7624 0.1812 0.144 0.004 0.448 0.020 0.156 0.228
#> TCGA-06-0122-01A-01 3 0.0146 0.8811 0.000 0.000 0.996 0.000 0.004 0.000
#> TCGA-06-0124-01A-01 3 0.2883 0.7970 0.000 0.032 0.864 0.016 0.088 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.2945 0.7933 0.000 0.824 0.000 0.020 0.156 0.000
#> TCGA-06-0143-01A-01 3 0.2821 0.7606 0.000 0.000 0.832 0.016 0.152 0.000
#> TCGA-06-0147-01A-01 2 0.2945 0.7933 0.000 0.824 0.000 0.020 0.156 0.000
#> TCGA-06-0149-01A-05 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0154-01A-02 3 0.1080 0.8640 0.000 0.032 0.960 0.004 0.004 0.000
#> TCGA-06-0164-01A-01 2 0.2945 0.7933 0.000 0.824 0.000 0.020 0.156 0.000
#> TCGA-06-0175-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.6517 0.5728 0.000 0.584 0.172 0.020 0.156 0.068
#> TCGA-06-0189-01A-05 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0291 0.8266 0.000 0.992 0.000 0.004 0.004 0.000
#> TCGA-06-0194-01A-01 2 0.2945 0.7933 0.000 0.824 0.000 0.020 0.156 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0210-01A-01 3 0.3151 0.5983 0.000 0.252 0.748 0.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0458 0.8193 0.000 0.984 0.016 0.000 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.5590 0.5862 0.000 0.608 0.216 0.020 0.156 0.000
#> TCGA-06-0412-01A-01 3 0.0000 0.8821 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0645-01A-01 3 0.3717 0.7201 0.000 0.040 0.792 0.016 0.152 0.000
#> TCGA-08-0346-01A-01 2 0.1615 0.8006 0.000 0.928 0.064 0.004 0.004 0.000
#> TCGA-08-0352-01A-01 3 0.2821 0.7606 0.000 0.000 0.832 0.016 0.152 0.000
#> TCGA-08-0360-01A-01 2 0.3086 0.7916 0.000 0.820 0.004 0.020 0.156 0.000
#> TCGA-08-0390-01A-01 2 0.3604 0.6685 0.000 0.788 0.000 0.008 0.036 0.168
#> TCGA-08-0392-01A-01 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.2945 0.7933 0.000 0.824 0.000 0.020 0.156 0.000
#> TCGA-08-0510-01A-01 3 0.3606 0.5208 0.000 0.284 0.708 0.004 0.004 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8271 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 3 0.3843 0.2918 0.000 0.452 0.548 0.000 0.000 0.000
#> TCGA-12-0620-01A-01 3 0.0363 0.8771 0.000 0.012 0.988 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> SD:pam 170 9.46e-28 2
#> SD:pam 165 2.57e-38 3
#> SD:pam 154 9.07e-55 4
#> SD:pam 137 7.39e-50 5
#> SD:pam 144 4.55e-53 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "mclust"]
# you can also extract it by
# res = res_list["SD:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.917 0.937 0.974 0.4990 0.501 0.501
#> 3 3 0.504 0.639 0.796 0.2686 0.783 0.589
#> 4 4 0.535 0.675 0.798 0.1586 0.813 0.515
#> 5 5 0.786 0.842 0.895 0.0560 0.902 0.656
#> 6 6 0.789 0.721 0.847 0.0408 0.905 0.639
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0048-01A-01 1 0.2948 0.923 0.948 0.052
#> TCGA-02-0060-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0376 0.967 0.996 0.004
#> TCGA-02-0084-01A-03 1 0.6247 0.806 0.844 0.156
#> TCGA-02-0087-01A-01 1 0.0376 0.967 0.996 0.004
#> TCGA-02-0104-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0325-01A-01 1 0.0376 0.967 0.996 0.004
#> TCGA-02-0338-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0128-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0166-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0174-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0646-01A-01 1 0.0376 0.967 0.996 0.004
#> TCGA-06-0648-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0348-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0353-01A-01 2 0.9580 0.387 0.380 0.620
#> TCGA-08-0359-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0089-01A-01 1 0.5946 0.825 0.856 0.144
#> TCGA-02-0113-01A-01 2 0.6531 0.787 0.168 0.832
#> TCGA-02-0115-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-02-0451-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0132-01A-02 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0133-01A-02 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0138-01A-02 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0160-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0162-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0167-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0171-01A-02 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0173-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0179-01A-02 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0182-01A-01 2 0.9710 0.333 0.400 0.600
#> TCGA-06-0185-01A-01 2 0.9710 0.333 0.400 0.600
#> TCGA-06-0195-01B-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0208-01B-01 1 0.9710 0.339 0.600 0.400
#> TCGA-06-0214-01A-02 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0219-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0221-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0237-01A-02 1 0.0000 0.970 1.000 0.000
#> TCGA-06-0240-01A-02 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0349-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0380-01A-01 1 0.0000 0.970 1.000 0.000
#> TCGA-08-0386-01A-01 1 0.8144 0.665 0.748 0.252
#> TCGA-08-0520-01A-01 1 0.9286 0.482 0.656 0.344
#> TCGA-02-0007-01A-01 1 0.8608 0.608 0.716 0.284
#> TCGA-02-0009-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0016-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0021-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0023-01B-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0027-01A-01 2 0.5519 0.838 0.128 0.872
#> TCGA-02-0038-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0043-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0070-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0102-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0260-01A-03 2 0.0376 0.971 0.004 0.996
#> TCGA-02-0269-01B-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0285-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0289-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0290-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0317-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0333-01A-02 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0422-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0430-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0125-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0126-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0137-01A-03 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0145-01A-04 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0148-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0187-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0211-01B-01 2 0.7219 0.742 0.200 0.800
#> TCGA-06-0402-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0246-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0357-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0358-01A-01 2 0.9491 0.417 0.368 0.632
#> TCGA-08-0375-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0511-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0514-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0529-01A-02 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0531-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0057-01A-01 1 0.9522 0.420 0.628 0.372
#> TCGA-02-0004-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0085-01A-01 1 0.1414 0.953 0.980 0.020
#> TCGA-02-0086-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-02-0326-01A-01 1 0.7376 0.738 0.792 0.208
#> TCGA-02-0337-01A-01 2 0.7056 0.751 0.192 0.808
#> TCGA-06-0122-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0147-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.975 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.975 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.975 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.3116 0.8015 0.892 0.000 0.108
#> TCGA-02-0010-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.4796 0.7137 0.780 0.000 0.220
#> TCGA-02-0014-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.5020 0.7530 0.796 0.012 0.192
#> TCGA-02-0047-01A-01 1 0.3879 0.7821 0.848 0.000 0.152
#> TCGA-02-0048-01A-01 3 0.5775 0.3116 0.260 0.012 0.728
#> TCGA-02-0060-01A-01 1 0.1964 0.8341 0.944 0.000 0.056
#> TCGA-02-0069-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.4974 0.7012 0.764 0.000 0.236
#> TCGA-02-0084-01A-03 1 0.5688 0.7402 0.788 0.044 0.168
#> TCGA-02-0087-01A-01 1 0.3192 0.8067 0.888 0.000 0.112
#> TCGA-02-0104-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.4539 0.7742 0.836 0.016 0.148
#> TCGA-02-0325-01A-01 1 0.5254 0.7374 0.736 0.000 0.264
#> TCGA-02-0338-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.4974 0.7012 0.764 0.000 0.236
#> TCGA-02-0439-01A-01 1 0.5254 0.7357 0.736 0.000 0.264
#> TCGA-02-0440-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.3918 0.7884 0.856 0.004 0.140
#> TCGA-06-0128-01A-01 1 0.0592 0.8417 0.988 0.000 0.012
#> TCGA-06-0129-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 1 0.3686 0.7885 0.860 0.000 0.140
#> TCGA-06-0166-01A-01 1 0.3752 0.7886 0.856 0.000 0.144
#> TCGA-06-0174-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.0424 0.8429 0.992 0.000 0.008
#> TCGA-06-0241-01A-02 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 1 0.6414 0.6458 0.716 0.036 0.248
#> TCGA-06-0648-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-08-0347-01A-01 1 0.3879 0.7821 0.848 0.000 0.152
#> TCGA-08-0348-01A-01 1 0.1411 0.8360 0.964 0.000 0.036
#> TCGA-08-0350-01A-01 1 0.0747 0.8415 0.984 0.000 0.016
#> TCGA-08-0353-01A-01 3 0.4978 0.4771 0.216 0.004 0.780
#> TCGA-08-0359-01A-01 1 0.2448 0.8235 0.924 0.000 0.076
#> TCGA-08-0385-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.8448 1.000 0.000 0.000
#> TCGA-02-0089-01A-01 3 0.9956 0.1801 0.328 0.296 0.376
#> TCGA-02-0113-01A-01 3 0.6895 0.5756 0.212 0.072 0.716
#> TCGA-02-0115-01A-01 3 0.9612 0.0805 0.372 0.204 0.424
#> TCGA-02-0451-01A-01 3 0.9561 0.0738 0.376 0.196 0.428
#> TCGA-06-0132-01A-02 1 0.6180 0.4296 0.584 0.000 0.416
#> TCGA-06-0133-01A-02 1 0.8840 0.1073 0.456 0.116 0.428
#> TCGA-06-0138-01A-02 1 0.7438 0.2923 0.536 0.036 0.428
#> TCGA-06-0160-01A-01 1 0.5553 0.6656 0.724 0.004 0.272
#> TCGA-06-0162-01A-01 1 0.7043 0.3174 0.532 0.020 0.448
#> TCGA-06-0167-01A-01 1 0.5553 0.6656 0.724 0.004 0.272
#> TCGA-06-0171-01A-02 1 0.6651 0.5488 0.656 0.024 0.320
#> TCGA-06-0173-01A-01 1 0.7534 0.2843 0.532 0.040 0.428
#> TCGA-06-0179-01A-02 1 0.6168 0.4387 0.588 0.000 0.412
#> TCGA-06-0182-01A-01 3 0.6416 0.3018 0.376 0.008 0.616
#> TCGA-06-0185-01A-01 3 0.6126 0.3292 0.352 0.004 0.644
#> TCGA-06-0195-01B-01 1 0.1411 0.8380 0.964 0.000 0.036
#> TCGA-06-0208-01B-01 3 0.7982 0.2130 0.376 0.068 0.556
#> TCGA-06-0214-01A-02 1 0.7883 0.2512 0.516 0.056 0.428
#> TCGA-06-0219-01A-01 1 0.6262 0.6003 0.696 0.020 0.284
#> TCGA-06-0221-01A-01 1 0.0892 0.8417 0.980 0.000 0.020
#> TCGA-06-0237-01A-02 1 0.7466 0.2449 0.520 0.036 0.444
#> TCGA-06-0240-01A-02 1 0.5553 0.6656 0.724 0.004 0.272
#> TCGA-08-0349-01A-01 1 0.7438 0.2923 0.536 0.036 0.428
#> TCGA-08-0380-01A-01 1 0.9112 0.0430 0.432 0.140 0.428
#> TCGA-08-0386-01A-01 3 0.6704 0.2594 0.376 0.016 0.608
#> TCGA-08-0520-01A-01 3 0.7820 0.1494 0.400 0.056 0.544
#> TCGA-02-0007-01A-01 3 0.6771 0.0505 0.440 0.012 0.548
#> TCGA-02-0009-01A-01 3 0.5465 0.6065 0.000 0.288 0.712
#> TCGA-02-0016-01A-01 3 0.5216 0.6242 0.000 0.260 0.740
#> TCGA-02-0021-01A-01 3 0.5465 0.6057 0.000 0.288 0.712
#> TCGA-02-0023-01B-01 3 0.5397 0.6153 0.000 0.280 0.720
#> TCGA-02-0027-01A-01 3 0.8298 0.5674 0.220 0.152 0.628
#> TCGA-02-0038-01A-01 3 0.6062 0.4764 0.000 0.384 0.616
#> TCGA-02-0043-01A-01 3 0.3607 0.5738 0.008 0.112 0.880
#> TCGA-02-0070-01A-01 3 0.6235 0.3198 0.000 0.436 0.564
#> TCGA-02-0102-01A-01 3 0.5560 0.5941 0.000 0.300 0.700
#> TCGA-02-0260-01A-03 3 0.1753 0.5774 0.000 0.048 0.952
#> TCGA-02-0269-01B-01 3 0.5058 0.6295 0.000 0.244 0.756
#> TCGA-02-0285-01A-01 3 0.6192 0.3641 0.000 0.420 0.580
#> TCGA-02-0289-01A-01 3 0.5397 0.6125 0.000 0.280 0.720
#> TCGA-02-0290-01A-01 3 0.6180 0.3870 0.000 0.416 0.584
#> TCGA-02-0317-01A-01 3 0.5058 0.6295 0.000 0.244 0.756
#> TCGA-02-0333-01A-02 3 0.5058 0.6295 0.000 0.244 0.756
#> TCGA-02-0422-01A-01 3 0.5560 0.5932 0.000 0.300 0.700
#> TCGA-02-0430-01A-01 3 0.5397 0.6118 0.000 0.280 0.720
#> TCGA-06-0125-01A-01 3 0.5058 0.6295 0.000 0.244 0.756
#> TCGA-06-0126-01A-01 3 0.5216 0.6242 0.000 0.260 0.740
#> TCGA-06-0137-01A-03 3 0.5254 0.6224 0.000 0.264 0.736
#> TCGA-06-0145-01A-04 2 0.6307 -0.0718 0.000 0.512 0.488
#> TCGA-06-0148-01A-01 3 0.6215 0.3426 0.000 0.428 0.572
#> TCGA-06-0187-01A-01 2 0.6302 -0.0421 0.000 0.520 0.480
#> TCGA-06-0211-01B-01 3 0.5020 0.5272 0.192 0.012 0.796
#> TCGA-06-0402-01A-01 3 0.5785 0.5502 0.000 0.332 0.668
#> TCGA-08-0246-01A-01 2 0.6260 0.0724 0.000 0.552 0.448
#> TCGA-08-0354-01A-01 3 0.6308 0.1635 0.000 0.492 0.508
#> TCGA-08-0355-01A-01 3 0.5560 0.5996 0.000 0.300 0.700
#> TCGA-08-0357-01A-01 3 0.5461 0.6303 0.008 0.244 0.748
#> TCGA-08-0358-01A-01 3 0.5012 0.5210 0.204 0.008 0.788
#> TCGA-08-0375-01A-01 3 0.2165 0.5838 0.000 0.064 0.936
#> TCGA-08-0511-01A-01 3 0.6111 0.4232 0.000 0.396 0.604
#> TCGA-08-0514-01A-01 3 0.6192 0.3694 0.000 0.420 0.580
#> TCGA-08-0518-01A-01 3 0.5859 0.5366 0.000 0.344 0.656
#> TCGA-08-0529-01A-02 3 0.5810 0.5458 0.000 0.336 0.664
#> TCGA-08-0531-01A-01 3 0.6111 0.4405 0.000 0.396 0.604
#> TCGA-02-0057-01A-01 3 0.9669 0.3732 0.212 0.380 0.408
#> TCGA-02-0004-01A-01 2 0.0000 0.8292 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.3686 0.7202 0.000 0.860 0.140
#> TCGA-02-0025-01A-01 2 0.0592 0.8239 0.000 0.988 0.012
#> TCGA-02-0033-01A-01 2 0.0424 0.8262 0.000 0.992 0.008
#> TCGA-02-0034-01A-01 2 0.0592 0.8239 0.000 0.988 0.012
#> TCGA-02-0039-01A-01 2 0.2959 0.7684 0.000 0.900 0.100
#> TCGA-02-0051-01A-01 2 0.0592 0.8239 0.000 0.988 0.012
#> TCGA-02-0054-01A-01 2 0.4842 0.5643 0.000 0.776 0.224
#> TCGA-02-0055-01A-01 2 0.0592 0.8239 0.000 0.988 0.012
#> TCGA-02-0059-01A-01 2 0.0424 0.8262 0.000 0.992 0.008
#> TCGA-02-0064-01A-01 2 0.3267 0.7834 0.000 0.884 0.116
#> TCGA-02-0075-01A-01 2 0.3816 0.7616 0.000 0.852 0.148
#> TCGA-02-0079-01A-03 2 0.1289 0.8238 0.000 0.968 0.032
#> TCGA-02-0085-01A-01 1 0.4575 0.7663 0.812 0.004 0.184
#> TCGA-02-0086-01A-01 2 0.3879 0.7550 0.000 0.848 0.152
#> TCGA-02-0099-01A-01 2 0.1163 0.8258 0.000 0.972 0.028
#> TCGA-02-0106-01A-01 2 0.0747 0.8295 0.000 0.984 0.016
#> TCGA-02-0107-01A-01 2 0.4002 0.7512 0.000 0.840 0.160
#> TCGA-02-0111-01A-01 2 0.0747 0.8298 0.000 0.984 0.016
#> TCGA-02-0326-01A-01 3 0.8334 0.0367 0.440 0.080 0.480
#> TCGA-02-0337-01A-01 2 0.7622 0.2573 0.332 0.608 0.060
#> TCGA-06-0122-01A-01 2 0.4931 0.6666 0.000 0.768 0.232
#> TCGA-06-0124-01A-01 2 0.4555 0.7030 0.000 0.800 0.200
#> TCGA-06-0130-01A-01 2 0.0592 0.8239 0.000 0.988 0.012
#> TCGA-06-0139-01A-01 2 0.0237 0.8304 0.000 0.996 0.004
#> TCGA-06-0143-01A-01 2 0.3619 0.7767 0.000 0.864 0.136
#> TCGA-06-0147-01A-01 2 0.0237 0.8304 0.000 0.996 0.004
#> TCGA-06-0149-01A-05 2 0.4750 0.6877 0.000 0.784 0.216
#> TCGA-06-0152-01A-02 3 0.6763 0.3456 0.012 0.436 0.552
#> TCGA-06-0154-01A-02 2 0.4178 0.7345 0.000 0.828 0.172
#> TCGA-06-0164-01A-01 2 0.0237 0.8304 0.000 0.996 0.004
#> TCGA-06-0175-01A-01 2 0.6235 0.0136 0.000 0.564 0.436
#> TCGA-06-0176-01A-03 2 0.0592 0.8239 0.000 0.988 0.012
#> TCGA-06-0184-01A-01 2 0.4062 0.6984 0.000 0.836 0.164
#> TCGA-06-0189-01A-05 2 0.0237 0.8304 0.000 0.996 0.004
#> TCGA-06-0190-01A-01 2 0.0237 0.8304 0.000 0.996 0.004
#> TCGA-06-0194-01A-01 2 0.0424 0.8307 0.000 0.992 0.008
#> TCGA-06-0197-01A-02 2 0.0747 0.8295 0.000 0.984 0.016
#> TCGA-06-0210-01A-01 2 0.4452 0.7173 0.000 0.808 0.192
#> TCGA-06-0397-01A-01 2 0.0892 0.8297 0.000 0.980 0.020
#> TCGA-06-0409-01A-02 2 0.4002 0.7495 0.000 0.840 0.160
#> TCGA-06-0412-01A-01 2 0.5016 0.6524 0.000 0.760 0.240
#> TCGA-06-0644-01A-02 2 0.0424 0.8262 0.000 0.992 0.008
#> TCGA-06-0645-01A-01 2 0.0747 0.8298 0.000 0.984 0.016
#> TCGA-08-0346-01A-01 2 0.3192 0.7866 0.000 0.888 0.112
#> TCGA-08-0352-01A-01 2 0.4974 0.6647 0.000 0.764 0.236
#> TCGA-08-0360-01A-01 2 0.0237 0.8304 0.000 0.996 0.004
#> TCGA-08-0390-01A-01 2 0.3686 0.7239 0.000 0.860 0.140
#> TCGA-08-0392-01A-01 2 0.0592 0.8239 0.000 0.988 0.012
#> TCGA-08-0509-01A-01 2 0.0892 0.8291 0.000 0.980 0.020
#> TCGA-08-0510-01A-01 2 0.5291 0.5991 0.000 0.732 0.268
#> TCGA-08-0512-01A-01 2 0.0237 0.8304 0.000 0.996 0.004
#> TCGA-08-0522-01A-01 2 0.0424 0.8262 0.000 0.992 0.008
#> TCGA-12-0619-01A-01 2 0.0424 0.8307 0.000 0.992 0.008
#> TCGA-12-0620-01A-01 2 0.6062 0.2819 0.000 0.616 0.384
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.4999 0.0698 0.508 0.000 0.000 0.492
#> TCGA-02-0010-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.4830 0.3220 0.608 0.000 0.000 0.392
#> TCGA-02-0014-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 4 0.5147 0.6458 0.200 0.000 0.060 0.740
#> TCGA-02-0047-01A-01 4 0.5137 0.6413 0.244 0.000 0.040 0.716
#> TCGA-02-0048-01A-01 4 0.6075 0.6700 0.148 0.000 0.168 0.684
#> TCGA-02-0060-01A-01 4 0.5050 0.1794 0.408 0.000 0.004 0.588
#> TCGA-02-0069-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0188 0.8941 0.996 0.000 0.000 0.004
#> TCGA-02-0080-01A-01 1 0.4830 0.3220 0.608 0.000 0.000 0.392
#> TCGA-02-0084-01A-03 4 0.6936 0.6630 0.224 0.000 0.188 0.588
#> TCGA-02-0087-01A-01 1 0.7219 -0.1770 0.488 0.000 0.148 0.364
#> TCGA-02-0104-01A-01 1 0.0188 0.8941 0.996 0.000 0.000 0.004
#> TCGA-02-0114-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 4 0.7072 0.6256 0.268 0.000 0.172 0.560
#> TCGA-02-0325-01A-01 4 0.6845 0.5973 0.236 0.000 0.168 0.596
#> TCGA-02-0338-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.4830 0.3220 0.608 0.000 0.000 0.392
#> TCGA-02-0439-01A-01 4 0.3946 0.6423 0.020 0.000 0.168 0.812
#> TCGA-02-0440-01A-01 1 0.0188 0.8941 0.996 0.000 0.000 0.004
#> TCGA-02-0446-01A-01 4 0.5628 0.3805 0.420 0.000 0.024 0.556
#> TCGA-06-0128-01A-01 1 0.4564 0.3926 0.672 0.000 0.000 0.328
#> TCGA-06-0129-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0188 0.8931 0.996 0.000 0.000 0.004
#> TCGA-06-0156-01A-01 4 0.7059 0.5589 0.332 0.000 0.140 0.528
#> TCGA-06-0166-01A-01 4 0.7184 0.5779 0.316 0.000 0.160 0.524
#> TCGA-06-0174-01A-01 1 0.0188 0.8941 0.996 0.000 0.000 0.004
#> TCGA-06-0177-01A-01 1 0.0188 0.8941 0.996 0.000 0.000 0.004
#> TCGA-06-0238-01A-02 1 0.2647 0.7773 0.880 0.000 0.000 0.120
#> TCGA-06-0241-01A-02 1 0.0188 0.8941 0.996 0.000 0.000 0.004
#> TCGA-06-0410-01A-01 1 0.0188 0.8941 0.996 0.000 0.000 0.004
#> TCGA-06-0413-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0188 0.8941 0.996 0.000 0.000 0.004
#> TCGA-06-0646-01A-01 4 0.5923 0.6788 0.128 0.000 0.176 0.696
#> TCGA-06-0648-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0336 0.8911 0.992 0.000 0.000 0.008
#> TCGA-08-0347-01A-01 4 0.6065 0.6832 0.140 0.000 0.176 0.684
#> TCGA-08-0348-01A-01 1 0.3972 0.5909 0.788 0.000 0.008 0.204
#> TCGA-08-0350-01A-01 1 0.0188 0.8941 0.996 0.000 0.000 0.004
#> TCGA-08-0353-01A-01 3 0.4509 0.4615 0.004 0.000 0.708 0.288
#> TCGA-08-0359-01A-01 4 0.4955 0.2858 0.444 0.000 0.000 0.556
#> TCGA-08-0385-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0188 0.8941 0.996 0.000 0.000 0.004
#> TCGA-08-0524-01A-01 1 0.0000 0.8942 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0188 0.8941 0.996 0.000 0.000 0.004
#> TCGA-12-0618-01A-01 1 0.0469 0.8875 0.988 0.000 0.000 0.012
#> TCGA-02-0089-01A-01 3 0.7506 -0.2365 0.016 0.116 0.440 0.428
#> TCGA-02-0113-01A-01 3 0.3822 0.6546 0.016 0.008 0.836 0.140
#> TCGA-02-0115-01A-01 4 0.6885 0.6062 0.016 0.116 0.244 0.624
#> TCGA-02-0451-01A-01 4 0.6404 0.6493 0.016 0.100 0.208 0.676
#> TCGA-06-0132-01A-02 4 0.5102 0.7154 0.100 0.000 0.136 0.764
#> TCGA-06-0133-01A-02 4 0.5321 0.6763 0.004 0.096 0.144 0.756
#> TCGA-06-0138-01A-02 4 0.3647 0.7038 0.108 0.000 0.040 0.852
#> TCGA-06-0160-01A-01 4 0.4564 0.2987 0.328 0.000 0.000 0.672
#> TCGA-06-0162-01A-01 4 0.5140 0.7133 0.096 0.000 0.144 0.760
#> TCGA-06-0167-01A-01 4 0.4564 0.2987 0.328 0.000 0.000 0.672
#> TCGA-06-0171-01A-02 4 0.3647 0.7038 0.108 0.000 0.040 0.852
#> TCGA-06-0173-01A-01 4 0.5010 0.7109 0.108 0.000 0.120 0.772
#> TCGA-06-0179-01A-02 4 0.5151 0.7153 0.100 0.000 0.140 0.760
#> TCGA-06-0182-01A-01 3 0.5459 0.0784 0.016 0.000 0.552 0.432
#> TCGA-06-0185-01A-01 3 0.4567 0.4967 0.016 0.000 0.740 0.244
#> TCGA-06-0195-01B-01 4 0.4933 0.1558 0.432 0.000 0.000 0.568
#> TCGA-06-0208-01B-01 4 0.7282 0.3657 0.016 0.100 0.380 0.504
#> TCGA-06-0214-01A-02 4 0.5590 0.6933 0.020 0.088 0.136 0.756
#> TCGA-06-0219-01A-01 4 0.3972 0.6399 0.204 0.000 0.008 0.788
#> TCGA-06-0221-01A-01 1 0.4072 0.6039 0.748 0.000 0.000 0.252
#> TCGA-06-0237-01A-02 4 0.3863 0.6906 0.028 0.000 0.144 0.828
#> TCGA-06-0240-01A-02 4 0.4564 0.2987 0.328 0.000 0.000 0.672
#> TCGA-08-0349-01A-01 4 0.4079 0.6815 0.020 0.000 0.180 0.800
#> TCGA-08-0380-01A-01 4 0.5983 0.6742 0.016 0.100 0.164 0.720
#> TCGA-08-0386-01A-01 4 0.4933 0.5898 0.016 0.000 0.296 0.688
#> TCGA-08-0520-01A-01 4 0.6147 0.6696 0.016 0.100 0.180 0.704
#> TCGA-02-0007-01A-01 4 0.5047 0.5645 0.016 0.000 0.316 0.668
#> TCGA-02-0009-01A-01 3 0.0592 0.7701 0.000 0.016 0.984 0.000
#> TCGA-02-0016-01A-01 3 0.0000 0.7646 0.000 0.000 1.000 0.000
#> TCGA-02-0021-01A-01 3 0.0000 0.7646 0.000 0.000 1.000 0.000
#> TCGA-02-0023-01B-01 3 0.0844 0.7661 0.004 0.012 0.980 0.004
#> TCGA-02-0027-01A-01 4 0.4643 0.4882 0.000 0.000 0.344 0.656
#> TCGA-02-0038-01A-01 3 0.3156 0.7563 0.000 0.068 0.884 0.048
#> TCGA-02-0043-01A-01 3 0.5462 0.7020 0.000 0.112 0.736 0.152
#> TCGA-02-0070-01A-01 3 0.4356 0.7446 0.000 0.148 0.804 0.048
#> TCGA-02-0102-01A-01 3 0.1867 0.7698 0.000 0.072 0.928 0.000
#> TCGA-02-0260-01A-03 3 0.2345 0.6820 0.000 0.000 0.900 0.100
#> TCGA-02-0269-01B-01 3 0.0000 0.7646 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 3 0.4874 0.7224 0.000 0.180 0.764 0.056
#> TCGA-02-0289-01A-01 3 0.0188 0.7664 0.000 0.004 0.996 0.000
#> TCGA-02-0290-01A-01 3 0.5384 0.6992 0.000 0.196 0.728 0.076
#> TCGA-02-0317-01A-01 3 0.0000 0.7646 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.7646 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 3 0.0817 0.7713 0.000 0.024 0.976 0.000
#> TCGA-02-0430-01A-01 3 0.1637 0.7720 0.000 0.060 0.940 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.7646 0.000 0.000 1.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.7646 0.000 0.000 1.000 0.000
#> TCGA-06-0137-01A-03 3 0.0188 0.7664 0.000 0.004 0.996 0.000
#> TCGA-06-0145-01A-04 3 0.3400 0.7202 0.000 0.180 0.820 0.000
#> TCGA-06-0148-01A-01 3 0.4387 0.7460 0.000 0.144 0.804 0.052
#> TCGA-06-0187-01A-01 3 0.3528 0.7122 0.000 0.192 0.808 0.000
#> TCGA-06-0211-01B-01 3 0.4428 0.4832 0.004 0.000 0.720 0.276
#> TCGA-06-0402-01A-01 3 0.4312 0.7485 0.000 0.132 0.812 0.056
#> TCGA-08-0246-01A-01 3 0.3972 0.7041 0.000 0.204 0.788 0.008
#> TCGA-08-0354-01A-01 3 0.5585 0.6879 0.000 0.204 0.712 0.084
#> TCGA-08-0355-01A-01 3 0.1109 0.7717 0.000 0.028 0.968 0.004
#> TCGA-08-0357-01A-01 3 0.0188 0.7637 0.000 0.000 0.996 0.004
#> TCGA-08-0358-01A-01 3 0.4594 0.4747 0.008 0.000 0.712 0.280
#> TCGA-08-0375-01A-01 3 0.2281 0.6859 0.000 0.000 0.904 0.096
#> TCGA-08-0511-01A-01 3 0.1022 0.7723 0.000 0.032 0.968 0.000
#> TCGA-08-0514-01A-01 3 0.3486 0.7152 0.000 0.188 0.812 0.000
#> TCGA-08-0518-01A-01 3 0.1940 0.7706 0.000 0.076 0.924 0.000
#> TCGA-08-0529-01A-02 3 0.1211 0.7737 0.000 0.040 0.960 0.000
#> TCGA-08-0531-01A-01 3 0.2216 0.7665 0.000 0.092 0.908 0.000
#> TCGA-02-0057-01A-01 4 0.7188 0.2972 0.000 0.136 0.432 0.432
#> TCGA-02-0004-01A-01 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.5966 0.4708 0.000 0.624 0.060 0.316
#> TCGA-02-0025-01A-01 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.5298 0.6183 0.000 0.708 0.048 0.244
#> TCGA-02-0051-01A-01 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.6738 0.3246 0.000 0.544 0.104 0.352
#> TCGA-02-0055-01A-01 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.3485 0.8239 0.000 0.856 0.116 0.028
#> TCGA-02-0075-01A-01 2 0.3278 0.8211 0.000 0.864 0.116 0.020
#> TCGA-02-0079-01A-03 2 0.5235 0.6276 0.000 0.716 0.048 0.236
#> TCGA-02-0085-01A-01 4 0.5102 0.6634 0.220 0.000 0.048 0.732
#> TCGA-02-0086-01A-01 2 0.2530 0.8275 0.000 0.888 0.112 0.000
#> TCGA-02-0099-01A-01 2 0.5687 0.5906 0.000 0.684 0.068 0.248
#> TCGA-02-0106-01A-01 2 0.2345 0.8337 0.000 0.900 0.100 0.000
#> TCGA-02-0107-01A-01 2 0.5867 0.7164 0.000 0.688 0.096 0.216
#> TCGA-02-0111-01A-01 2 0.2973 0.8354 0.000 0.884 0.096 0.020
#> TCGA-02-0326-01A-01 4 0.4867 0.6341 0.032 0.000 0.232 0.736
#> TCGA-02-0337-01A-01 4 0.8223 0.2996 0.112 0.372 0.060 0.456
#> TCGA-06-0122-01A-01 3 0.7154 0.1580 0.000 0.428 0.440 0.132
#> TCGA-06-0124-01A-01 2 0.3674 0.8136 0.000 0.848 0.116 0.036
#> TCGA-06-0130-01A-01 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.2281 0.8369 0.000 0.904 0.096 0.000
#> TCGA-06-0143-01A-01 2 0.7706 0.2330 0.000 0.436 0.328 0.236
#> TCGA-06-0147-01A-01 2 0.2216 0.8367 0.000 0.908 0.092 0.000
#> TCGA-06-0149-01A-05 3 0.6728 0.5613 0.000 0.268 0.596 0.136
#> TCGA-06-0152-01A-02 3 0.6750 0.5886 0.000 0.180 0.612 0.208
#> TCGA-06-0154-01A-02 2 0.2589 0.8231 0.000 0.884 0.116 0.000
#> TCGA-06-0164-01A-01 2 0.2281 0.8369 0.000 0.904 0.096 0.000
#> TCGA-06-0175-01A-01 3 0.7197 0.2558 0.000 0.140 0.468 0.392
#> TCGA-06-0176-01A-03 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 3 0.7688 0.2342 0.000 0.364 0.416 0.220
#> TCGA-06-0189-01A-05 2 0.2281 0.8369 0.000 0.904 0.096 0.000
#> TCGA-06-0190-01A-01 2 0.2345 0.8337 0.000 0.900 0.100 0.000
#> TCGA-06-0194-01A-01 2 0.2281 0.8369 0.000 0.904 0.096 0.000
#> TCGA-06-0197-01A-02 2 0.2281 0.8369 0.000 0.904 0.096 0.000
#> TCGA-06-0210-01A-01 2 0.3877 0.8088 0.000 0.840 0.112 0.048
#> TCGA-06-0397-01A-01 2 0.2345 0.8337 0.000 0.900 0.100 0.000
#> TCGA-06-0409-01A-02 2 0.3877 0.8247 0.000 0.840 0.112 0.048
#> TCGA-06-0412-01A-01 2 0.6445 -0.0590 0.000 0.488 0.444 0.068
#> TCGA-06-0644-01A-02 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.4295 0.6509 0.000 0.752 0.008 0.240
#> TCGA-08-0346-01A-01 2 0.3278 0.8224 0.000 0.864 0.116 0.020
#> TCGA-08-0352-01A-01 3 0.7099 0.5017 0.000 0.280 0.552 0.168
#> TCGA-08-0360-01A-01 2 0.2281 0.8369 0.000 0.904 0.096 0.000
#> TCGA-08-0390-01A-01 2 0.6121 0.4083 0.000 0.588 0.060 0.352
#> TCGA-08-0392-01A-01 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.4840 0.6679 0.000 0.732 0.028 0.240
#> TCGA-08-0510-01A-01 3 0.6797 0.4262 0.000 0.356 0.536 0.108
#> TCGA-08-0512-01A-01 2 0.2345 0.8337 0.000 0.900 0.100 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8334 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0592 0.8358 0.000 0.984 0.016 0.000
#> TCGA-12-0620-01A-01 3 0.6961 0.4616 0.000 0.316 0.548 0.136
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 4 0.3242 0.7813 0.172 0.000 0.000 0.816 0.012
#> TCGA-02-0010-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-02-0011-01B-01 4 0.3928 0.6679 0.296 0.000 0.000 0.700 0.004
#> TCGA-02-0014-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-02-0024-01B-01 1 0.1410 0.9519 0.940 0.000 0.000 0.000 0.060
#> TCGA-02-0026-01B-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-02-0028-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-02-0046-01A-01 4 0.3047 0.8297 0.084 0.000 0.044 0.868 0.004
#> TCGA-02-0047-01A-01 4 0.3089 0.8309 0.076 0.000 0.040 0.872 0.012
#> TCGA-02-0048-01A-01 4 0.3301 0.8146 0.072 0.000 0.080 0.848 0.000
#> TCGA-02-0060-01A-01 4 0.2864 0.8081 0.136 0.000 0.000 0.852 0.012
#> TCGA-02-0069-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-02-0074-01A-01 1 0.0162 0.9509 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0080-01A-01 4 0.3607 0.7167 0.244 0.000 0.000 0.752 0.004
#> TCGA-02-0084-01A-03 4 0.4499 0.7741 0.060 0.000 0.164 0.764 0.012
#> TCGA-02-0087-01A-01 4 0.4958 0.7927 0.176 0.000 0.084 0.728 0.012
#> TCGA-02-0104-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-02-0114-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-02-0281-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-02-0321-01A-01 4 0.2899 0.8132 0.028 0.004 0.096 0.872 0.000
#> TCGA-02-0325-01A-01 4 0.5912 0.7254 0.196 0.000 0.184 0.616 0.004
#> TCGA-02-0338-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-02-0339-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-02-0432-01A-02 4 0.3934 0.7010 0.244 0.000 0.000 0.740 0.016
#> TCGA-02-0439-01A-01 4 0.2472 0.8304 0.036 0.000 0.044 0.908 0.012
#> TCGA-02-0440-01A-01 1 0.0162 0.9509 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0446-01A-01 4 0.3620 0.8204 0.128 0.000 0.032 0.828 0.012
#> TCGA-06-0128-01A-01 4 0.3809 0.7158 0.256 0.000 0.000 0.736 0.008
#> TCGA-06-0129-01A-01 1 0.0290 0.9521 0.992 0.000 0.000 0.000 0.008
#> TCGA-06-0146-01A-01 1 0.0324 0.9512 0.992 0.000 0.000 0.004 0.004
#> TCGA-06-0156-01A-01 4 0.2710 0.8282 0.040 0.004 0.044 0.900 0.012
#> TCGA-06-0166-01A-01 4 0.2675 0.8266 0.032 0.008 0.044 0.904 0.012
#> TCGA-06-0174-01A-01 1 0.1205 0.9170 0.956 0.000 0.000 0.040 0.004
#> TCGA-06-0177-01A-01 1 0.0162 0.9509 0.996 0.000 0.000 0.000 0.004
#> TCGA-06-0238-01A-02 1 0.4252 0.4848 0.700 0.000 0.000 0.280 0.020
#> TCGA-06-0241-01A-02 1 0.0162 0.9509 0.996 0.000 0.000 0.000 0.004
#> TCGA-06-0410-01A-01 1 0.0162 0.9509 0.996 0.000 0.000 0.000 0.004
#> TCGA-06-0413-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-06-0414-01A-01 1 0.0162 0.9509 0.996 0.000 0.000 0.000 0.004
#> TCGA-06-0646-01A-01 4 0.3262 0.7827 0.000 0.036 0.124 0.840 0.000
#> TCGA-06-0648-01A-01 1 0.0162 0.9509 0.996 0.000 0.000 0.000 0.004
#> TCGA-08-0245-01A-01 1 0.0162 0.9509 0.996 0.000 0.000 0.000 0.004
#> TCGA-08-0344-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-08-0347-01A-01 4 0.3699 0.7971 0.036 0.000 0.128 0.824 0.012
#> TCGA-08-0348-01A-01 4 0.4134 0.6851 0.284 0.000 0.004 0.704 0.008
#> TCGA-08-0350-01A-01 1 0.0162 0.9509 0.996 0.000 0.000 0.000 0.004
#> TCGA-08-0353-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0359-01A-01 4 0.2771 0.8126 0.128 0.000 0.000 0.860 0.012
#> TCGA-08-0385-01A-01 1 0.1410 0.9521 0.940 0.000 0.000 0.000 0.060
#> TCGA-08-0517-01A-01 1 0.0324 0.9482 0.992 0.000 0.000 0.004 0.004
#> TCGA-08-0524-01A-01 1 0.1478 0.9517 0.936 0.000 0.000 0.000 0.064
#> TCGA-12-0616-01A-01 1 0.0162 0.9509 0.996 0.000 0.000 0.000 0.004
#> TCGA-12-0618-01A-01 1 0.0000 0.9514 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 3 0.4240 0.7140 0.000 0.036 0.736 0.228 0.000
#> TCGA-02-0113-01A-01 3 0.1408 0.9081 0.000 0.008 0.948 0.044 0.000
#> TCGA-02-0115-01A-01 4 0.4522 0.4644 0.000 0.024 0.316 0.660 0.000
#> TCGA-02-0451-01A-01 4 0.3238 0.7758 0.000 0.028 0.136 0.836 0.000
#> TCGA-06-0132-01A-02 4 0.2139 0.8148 0.032 0.000 0.000 0.916 0.052
#> TCGA-06-0133-01A-02 4 0.2511 0.8136 0.000 0.024 0.024 0.908 0.044
#> TCGA-06-0138-01A-02 4 0.0865 0.8164 0.000 0.024 0.004 0.972 0.000
#> TCGA-06-0160-01A-01 4 0.3631 0.7935 0.104 0.000 0.000 0.824 0.072
#> TCGA-06-0162-01A-01 4 0.1121 0.8086 0.000 0.000 0.000 0.956 0.044
#> TCGA-06-0167-01A-01 4 0.3631 0.7935 0.104 0.000 0.000 0.824 0.072
#> TCGA-06-0171-01A-02 4 0.0162 0.8167 0.000 0.000 0.000 0.996 0.004
#> TCGA-06-0173-01A-01 4 0.2654 0.8049 0.000 0.032 0.084 0.884 0.000
#> TCGA-06-0179-01A-02 4 0.2139 0.8148 0.032 0.000 0.000 0.916 0.052
#> TCGA-06-0182-01A-01 3 0.4135 0.4789 0.000 0.004 0.656 0.340 0.000
#> TCGA-06-0185-01A-01 3 0.1831 0.8924 0.000 0.004 0.920 0.076 0.000
#> TCGA-06-0195-01B-01 4 0.3575 0.7926 0.120 0.000 0.000 0.824 0.056
#> TCGA-06-0208-01B-01 3 0.4304 0.1470 0.000 0.000 0.516 0.484 0.000
#> TCGA-06-0214-01A-02 4 0.2864 0.7919 0.000 0.024 0.112 0.864 0.000
#> TCGA-06-0219-01A-01 4 0.1121 0.8086 0.000 0.000 0.000 0.956 0.044
#> TCGA-06-0221-01A-01 4 0.5104 0.6145 0.308 0.000 0.000 0.632 0.060
#> TCGA-06-0237-01A-02 4 0.1597 0.8202 0.000 0.000 0.048 0.940 0.012
#> TCGA-06-0240-01A-02 4 0.3631 0.7935 0.104 0.000 0.000 0.824 0.072
#> TCGA-08-0349-01A-01 4 0.1270 0.8188 0.000 0.000 0.052 0.948 0.000
#> TCGA-08-0380-01A-01 4 0.2300 0.8114 0.000 0.024 0.072 0.904 0.000
#> TCGA-08-0386-01A-01 3 0.4161 0.4055 0.000 0.000 0.608 0.392 0.000
#> TCGA-08-0520-01A-01 4 0.4150 0.3178 0.000 0.000 0.388 0.612 0.000
#> TCGA-02-0007-01A-01 4 0.3684 0.6171 0.000 0.000 0.280 0.720 0.000
#> TCGA-02-0009-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0021-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.1121 0.9096 0.000 0.000 0.956 0.044 0.000
#> TCGA-02-0027-01A-01 3 0.3336 0.7161 0.000 0.000 0.772 0.228 0.000
#> TCGA-02-0038-01A-01 3 0.1484 0.9069 0.000 0.008 0.944 0.048 0.000
#> TCGA-02-0043-01A-01 3 0.0703 0.9095 0.000 0.000 0.976 0.024 0.000
#> TCGA-02-0070-01A-01 3 0.0794 0.9077 0.000 0.000 0.972 0.028 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0285-01A-01 3 0.0963 0.9123 0.000 0.000 0.964 0.036 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0290-01A-01 3 0.1522 0.9070 0.000 0.012 0.944 0.044 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0422-01A-01 3 0.0290 0.9171 0.000 0.000 0.992 0.008 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0145-01A-04 3 0.0290 0.9171 0.000 0.000 0.992 0.008 0.000
#> TCGA-06-0148-01A-01 3 0.0794 0.9077 0.000 0.000 0.972 0.028 0.000
#> TCGA-06-0187-01A-01 3 0.1408 0.9081 0.000 0.008 0.948 0.044 0.000
#> TCGA-06-0211-01B-01 3 0.0609 0.9163 0.000 0.000 0.980 0.020 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.1408 0.9081 0.000 0.008 0.948 0.044 0.000
#> TCGA-08-0354-01A-01 3 0.1818 0.9024 0.000 0.024 0.932 0.044 0.000
#> TCGA-08-0355-01A-01 3 0.1282 0.9089 0.000 0.004 0.952 0.044 0.000
#> TCGA-08-0357-01A-01 3 0.1043 0.9111 0.000 0.000 0.960 0.040 0.000
#> TCGA-08-0358-01A-01 3 0.0451 0.9148 0.008 0.000 0.988 0.004 0.000
#> TCGA-08-0375-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0511-01A-01 3 0.1043 0.9111 0.000 0.000 0.960 0.040 0.000
#> TCGA-08-0514-01A-01 3 0.1282 0.9089 0.000 0.004 0.952 0.044 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.9166 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.0404 0.9167 0.000 0.000 0.988 0.012 0.000
#> TCGA-02-0057-01A-01 3 0.4276 0.6956 0.000 0.032 0.724 0.244 0.000
#> TCGA-02-0004-01A-01 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-02-0006-01B-01 2 0.3593 0.7465 0.000 0.828 0.084 0.088 0.000
#> TCGA-02-0025-01A-01 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-02-0033-01A-01 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-02-0034-01A-01 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-02-0039-01A-01 2 0.1670 0.8472 0.000 0.936 0.012 0.052 0.000
#> TCGA-02-0051-01A-01 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-02-0054-01A-01 2 0.3970 0.7195 0.000 0.800 0.096 0.104 0.000
#> TCGA-02-0055-01A-01 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-02-0059-01A-01 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-02-0064-01A-01 2 0.0880 0.8854 0.000 0.968 0.000 0.000 0.032
#> TCGA-02-0075-01A-01 2 0.0880 0.8854 0.000 0.968 0.000 0.000 0.032
#> TCGA-02-0079-01A-03 2 0.0880 0.8671 0.000 0.968 0.000 0.032 0.000
#> TCGA-02-0085-01A-01 4 0.3547 0.7963 0.008 0.032 0.108 0.844 0.008
#> TCGA-02-0086-01A-01 2 0.0703 0.8866 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0099-01A-01 2 0.1818 0.8414 0.000 0.932 0.024 0.044 0.000
#> TCGA-02-0106-01A-01 2 0.3109 0.6888 0.000 0.800 0.000 0.000 0.200
#> TCGA-02-0107-01A-01 2 0.0703 0.8866 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0111-01A-01 2 0.0404 0.8868 0.000 0.988 0.000 0.000 0.012
#> TCGA-02-0326-01A-01 4 0.3796 0.5610 0.000 0.000 0.300 0.700 0.000
#> TCGA-02-0337-01A-01 4 0.4553 0.3545 0.000 0.384 0.004 0.604 0.008
#> TCGA-06-0122-01A-01 3 0.4696 0.2312 0.000 0.428 0.556 0.016 0.000
#> TCGA-06-0124-01A-01 2 0.0609 0.8871 0.000 0.980 0.000 0.000 0.020
#> TCGA-06-0130-01A-01 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-06-0139-01A-01 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-06-0143-01A-01 2 0.3687 0.6789 0.000 0.792 0.180 0.028 0.000
#> TCGA-06-0147-01A-01 5 0.3395 0.8640 0.000 0.236 0.000 0.000 0.764
#> TCGA-06-0149-01A-05 3 0.3033 0.8600 0.000 0.084 0.864 0.052 0.000
#> TCGA-06-0152-01A-02 3 0.1830 0.9014 0.000 0.008 0.924 0.068 0.000
#> TCGA-06-0154-01A-02 2 0.0880 0.8854 0.000 0.968 0.000 0.000 0.032
#> TCGA-06-0164-01A-01 2 0.0880 0.8837 0.000 0.968 0.000 0.000 0.032
#> TCGA-06-0175-01A-01 2 0.5025 0.6039 0.000 0.704 0.172 0.124 0.000
#> TCGA-06-0176-01A-03 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-06-0184-01A-01 3 0.5484 0.5899 0.000 0.240 0.640 0.120 0.000
#> TCGA-06-0189-01A-05 2 0.0963 0.8819 0.000 0.964 0.000 0.000 0.036
#> TCGA-06-0190-01A-01 2 0.1043 0.8796 0.000 0.960 0.000 0.000 0.040
#> TCGA-06-0194-01A-01 2 0.0404 0.8867 0.000 0.988 0.000 0.000 0.012
#> TCGA-06-0197-01A-02 2 0.1043 0.8796 0.000 0.960 0.000 0.000 0.040
#> TCGA-06-0210-01A-01 2 0.0510 0.8767 0.000 0.984 0.000 0.016 0.000
#> TCGA-06-0397-01A-01 2 0.0880 0.8854 0.000 0.968 0.000 0.000 0.032
#> TCGA-06-0409-01A-02 2 0.0510 0.8871 0.000 0.984 0.000 0.000 0.016
#> TCGA-06-0412-01A-01 2 0.5504 0.0279 0.000 0.488 0.448 0.064 0.000
#> TCGA-06-0644-01A-02 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-06-0645-01A-01 2 0.0000 0.8833 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.8833 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0352-01A-01 3 0.3375 0.8411 0.000 0.104 0.840 0.056 0.000
#> TCGA-08-0360-01A-01 2 0.0880 0.8854 0.000 0.968 0.000 0.000 0.032
#> TCGA-08-0390-01A-01 2 0.1671 0.8320 0.000 0.924 0.000 0.076 0.000
#> TCGA-08-0392-01A-01 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-08-0509-01A-01 2 0.0162 0.8823 0.000 0.996 0.000 0.004 0.000
#> TCGA-08-0510-01A-01 3 0.3090 0.8576 0.000 0.088 0.860 0.052 0.000
#> TCGA-08-0512-01A-01 2 0.1121 0.8768 0.000 0.956 0.000 0.000 0.044
#> TCGA-08-0522-01A-01 5 0.2471 0.9907 0.000 0.136 0.000 0.000 0.864
#> TCGA-12-0619-01A-01 2 0.0880 0.8854 0.000 0.968 0.000 0.000 0.032
#> TCGA-12-0620-01A-01 2 0.4313 0.6762 0.000 0.760 0.172 0.068 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.4882 0.296 0.660 0.000 0.000 0.152 0.000 0.188
#> TCGA-02-0010-01A-01 1 0.3043 0.772 0.792 0.000 0.000 0.200 0.008 0.000
#> TCGA-02-0011-01B-01 1 0.3458 0.583 0.808 0.000 0.000 0.080 0.000 0.112
#> TCGA-02-0014-01A-01 1 0.3043 0.772 0.792 0.000 0.000 0.200 0.008 0.000
#> TCGA-02-0024-01B-01 1 0.2848 0.779 0.816 0.000 0.000 0.176 0.008 0.000
#> TCGA-02-0026-01B-01 1 0.2814 0.779 0.820 0.000 0.000 0.172 0.008 0.000
#> TCGA-02-0028-01A-01 1 0.2593 0.784 0.844 0.000 0.000 0.148 0.008 0.000
#> TCGA-02-0046-01A-01 6 0.3806 0.488 0.200 0.000 0.000 0.048 0.000 0.752
#> TCGA-02-0047-01A-01 6 0.4643 0.565 0.096 0.024 0.000 0.152 0.000 0.728
#> TCGA-02-0048-01A-01 6 0.3520 0.513 0.188 0.000 0.036 0.000 0.000 0.776
#> TCGA-02-0060-01A-01 6 0.5015 0.399 0.208 0.000 0.000 0.152 0.000 0.640
#> TCGA-02-0069-01A-01 1 0.3043 0.772 0.792 0.000 0.000 0.200 0.008 0.000
#> TCGA-02-0074-01A-01 1 0.0260 0.786 0.992 0.000 0.000 0.008 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.4602 0.402 0.696 0.000 0.000 0.160 0.000 0.144
#> TCGA-02-0084-01A-03 6 0.5063 0.568 0.088 0.024 0.020 0.152 0.000 0.716
#> TCGA-02-0087-01A-01 6 0.4849 0.457 0.188 0.000 0.000 0.148 0.000 0.664
#> TCGA-02-0104-01A-01 1 0.3043 0.772 0.792 0.000 0.000 0.200 0.008 0.000
#> TCGA-02-0114-01A-01 1 0.3043 0.772 0.792 0.000 0.000 0.200 0.008 0.000
#> TCGA-02-0281-01A-01 1 0.3012 0.774 0.796 0.000 0.000 0.196 0.008 0.000
#> TCGA-02-0321-01A-01 6 0.1863 0.677 0.036 0.000 0.000 0.044 0.000 0.920
#> TCGA-02-0325-01A-01 6 0.6922 0.146 0.196 0.000 0.176 0.132 0.000 0.496
#> TCGA-02-0338-01A-01 1 0.3043 0.772 0.792 0.000 0.000 0.200 0.008 0.000
#> TCGA-02-0339-01A-01 1 0.3043 0.772 0.792 0.000 0.000 0.200 0.008 0.000
#> TCGA-02-0432-01A-02 1 0.5276 0.127 0.540 0.000 0.000 0.348 0.000 0.112
#> TCGA-02-0439-01A-01 6 0.3652 0.635 0.056 0.016 0.000 0.120 0.000 0.808
#> TCGA-02-0440-01A-01 1 0.0777 0.776 0.972 0.000 0.000 0.024 0.000 0.004
#> TCGA-02-0446-01A-01 6 0.4889 0.518 0.136 0.016 0.000 0.152 0.000 0.696
#> TCGA-06-0128-01A-01 1 0.4771 0.253 0.648 0.000 0.000 0.096 0.000 0.256
#> TCGA-06-0129-01A-01 1 0.2048 0.789 0.880 0.000 0.000 0.120 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.1411 0.791 0.936 0.000 0.000 0.060 0.004 0.000
#> TCGA-06-0156-01A-01 6 0.4387 0.540 0.128 0.000 0.000 0.152 0.000 0.720
#> TCGA-06-0166-01A-01 6 0.4226 0.561 0.112 0.000 0.000 0.152 0.000 0.736
#> TCGA-06-0174-01A-01 1 0.1462 0.749 0.936 0.000 0.000 0.056 0.000 0.008
#> TCGA-06-0177-01A-01 1 0.0260 0.786 0.992 0.000 0.000 0.008 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.1408 0.758 0.944 0.000 0.000 0.020 0.000 0.036
#> TCGA-06-0241-01A-02 1 0.0000 0.788 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0405 0.784 0.988 0.000 0.000 0.008 0.000 0.004
#> TCGA-06-0413-01A-01 1 0.2848 0.779 0.816 0.000 0.000 0.176 0.008 0.000
#> TCGA-06-0414-01A-01 1 0.0260 0.786 0.992 0.000 0.000 0.008 0.000 0.000
#> TCGA-06-0646-01A-01 6 0.0891 0.687 0.000 0.024 0.000 0.008 0.000 0.968
#> TCGA-06-0648-01A-01 1 0.0000 0.788 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0260 0.788 0.992 0.000 0.000 0.008 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.3012 0.774 0.796 0.000 0.000 0.196 0.008 0.000
#> TCGA-08-0347-01A-01 6 0.4188 0.604 0.060 0.024 0.000 0.152 0.000 0.764
#> TCGA-08-0348-01A-01 1 0.5498 -0.242 0.464 0.000 0.000 0.128 0.000 0.408
#> TCGA-08-0350-01A-01 1 0.0520 0.783 0.984 0.000 0.000 0.008 0.000 0.008
#> TCGA-08-0353-01A-01 3 0.1141 0.853 0.000 0.000 0.948 0.000 0.000 0.052
#> TCGA-08-0359-01A-01 6 0.4671 0.491 0.160 0.000 0.000 0.152 0.000 0.688
#> TCGA-08-0385-01A-01 1 0.2006 0.789 0.892 0.000 0.000 0.104 0.004 0.000
#> TCGA-08-0517-01A-01 1 0.0508 0.783 0.984 0.000 0.000 0.004 0.000 0.012
#> TCGA-08-0524-01A-01 1 0.3043 0.772 0.792 0.000 0.000 0.200 0.008 0.000
#> TCGA-12-0616-01A-01 1 0.0692 0.779 0.976 0.000 0.000 0.020 0.000 0.004
#> TCGA-12-0618-01A-01 1 0.0291 0.788 0.992 0.000 0.000 0.004 0.000 0.004
#> TCGA-02-0089-01A-01 6 0.4535 -0.111 0.000 0.032 0.484 0.000 0.000 0.484
#> TCGA-02-0113-01A-01 3 0.3409 0.710 0.000 0.028 0.780 0.000 0.000 0.192
#> TCGA-02-0115-01A-01 6 0.3534 0.538 0.000 0.024 0.200 0.004 0.000 0.772
#> TCGA-02-0451-01A-01 6 0.1908 0.668 0.000 0.028 0.056 0.000 0.000 0.916
#> TCGA-06-0132-01A-02 6 0.3684 0.386 0.004 0.000 0.000 0.332 0.000 0.664
#> TCGA-06-0133-01A-02 6 0.3163 0.575 0.000 0.000 0.040 0.140 0.000 0.820
#> TCGA-06-0138-01A-02 6 0.0632 0.686 0.000 0.024 0.000 0.000 0.000 0.976
#> TCGA-06-0160-01A-01 4 0.4451 1.000 0.124 0.000 0.000 0.724 0.004 0.148
#> TCGA-06-0162-01A-01 6 0.2883 0.494 0.000 0.000 0.000 0.212 0.000 0.788
#> TCGA-06-0167-01A-01 4 0.4451 1.000 0.124 0.000 0.000 0.724 0.004 0.148
#> TCGA-06-0171-01A-02 6 0.0865 0.680 0.000 0.000 0.000 0.036 0.000 0.964
#> TCGA-06-0173-01A-01 6 0.0632 0.686 0.000 0.024 0.000 0.000 0.000 0.976
#> TCGA-06-0179-01A-02 6 0.3684 0.386 0.004 0.000 0.000 0.332 0.000 0.664
#> TCGA-06-0182-01A-01 3 0.4385 0.158 0.000 0.024 0.532 0.000 0.000 0.444
#> TCGA-06-0185-01A-01 3 0.4241 0.369 0.000 0.024 0.608 0.000 0.000 0.368
#> TCGA-06-0195-01B-01 1 0.5826 -0.265 0.472 0.000 0.000 0.324 0.000 0.204
#> TCGA-06-0208-01B-01 6 0.3508 0.439 0.000 0.000 0.292 0.004 0.000 0.704
#> TCGA-06-0214-01A-02 6 0.0858 0.685 0.000 0.028 0.004 0.000 0.000 0.968
#> TCGA-06-0219-01A-01 6 0.3163 0.517 0.004 0.000 0.000 0.232 0.000 0.764
#> TCGA-06-0221-01A-01 1 0.4911 0.240 0.624 0.000 0.000 0.276 0.000 0.100
#> TCGA-06-0237-01A-02 6 0.0935 0.679 0.000 0.000 0.032 0.004 0.000 0.964
#> TCGA-06-0240-01A-02 4 0.4451 1.000 0.124 0.000 0.000 0.724 0.004 0.148
#> TCGA-08-0349-01A-01 6 0.0632 0.686 0.000 0.024 0.000 0.000 0.000 0.976
#> TCGA-08-0380-01A-01 6 0.1498 0.679 0.000 0.028 0.032 0.000 0.000 0.940
#> TCGA-08-0386-01A-01 6 0.2971 0.606 0.020 0.004 0.144 0.000 0.000 0.832
#> TCGA-08-0520-01A-01 6 0.2911 0.597 0.000 0.024 0.144 0.000 0.000 0.832
#> TCGA-02-0007-01A-01 6 0.2487 0.657 0.032 0.000 0.092 0.000 0.000 0.876
#> TCGA-02-0009-01A-01 3 0.1501 0.862 0.000 0.000 0.924 0.076 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.1501 0.862 0.000 0.000 0.924 0.076 0.000 0.000
#> TCGA-02-0021-01A-01 3 0.1204 0.867 0.000 0.000 0.944 0.056 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.3280 0.749 0.000 0.028 0.808 0.004 0.000 0.160
#> TCGA-02-0027-01A-01 3 0.3563 0.441 0.000 0.000 0.664 0.000 0.000 0.336
#> TCGA-02-0038-01A-01 3 0.3175 0.744 0.000 0.028 0.808 0.000 0.000 0.164
#> TCGA-02-0043-01A-01 3 0.0260 0.867 0.000 0.008 0.992 0.000 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.0260 0.868 0.000 0.008 0.992 0.000 0.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.867 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.1444 0.864 0.000 0.000 0.928 0.072 0.000 0.000
#> TCGA-02-0269-01B-01 3 0.1501 0.862 0.000 0.000 0.924 0.076 0.000 0.000
#> TCGA-02-0285-01A-01 3 0.0891 0.860 0.000 0.024 0.968 0.000 0.000 0.008
#> TCGA-02-0289-01A-01 3 0.1501 0.862 0.000 0.000 0.924 0.076 0.000 0.000
#> TCGA-02-0290-01A-01 3 0.3634 0.557 0.000 0.296 0.696 0.000 0.000 0.008
#> TCGA-02-0317-01A-01 3 0.1501 0.862 0.000 0.000 0.924 0.076 0.000 0.000
#> TCGA-02-0333-01A-02 3 0.1501 0.862 0.000 0.000 0.924 0.076 0.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.867 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.867 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.1501 0.862 0.000 0.000 0.924 0.076 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.1444 0.864 0.000 0.000 0.928 0.072 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.1501 0.862 0.000 0.000 0.924 0.076 0.000 0.000
#> TCGA-06-0145-01A-04 3 0.1501 0.862 0.000 0.000 0.924 0.076 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.0146 0.868 0.000 0.004 0.996 0.000 0.000 0.000
#> TCGA-06-0187-01A-01 3 0.1787 0.839 0.000 0.068 0.920 0.004 0.000 0.008
#> TCGA-06-0211-01B-01 3 0.1434 0.851 0.012 0.000 0.940 0.000 0.000 0.048
#> TCGA-06-0402-01A-01 3 0.0260 0.867 0.000 0.008 0.992 0.000 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.2946 0.736 0.000 0.176 0.812 0.000 0.000 0.012
#> TCGA-08-0354-01A-01 3 0.3847 0.444 0.000 0.348 0.644 0.000 0.000 0.008
#> TCGA-08-0355-01A-01 3 0.3139 0.747 0.000 0.028 0.812 0.000 0.000 0.160
#> TCGA-08-0357-01A-01 3 0.0520 0.865 0.000 0.008 0.984 0.000 0.000 0.008
#> TCGA-08-0358-01A-01 3 0.1549 0.849 0.020 0.000 0.936 0.000 0.000 0.044
#> TCGA-08-0375-01A-01 3 0.1204 0.867 0.000 0.000 0.944 0.056 0.000 0.000
#> TCGA-08-0511-01A-01 3 0.0891 0.860 0.000 0.024 0.968 0.000 0.000 0.008
#> TCGA-08-0514-01A-01 3 0.0972 0.859 0.000 0.028 0.964 0.000 0.000 0.008
#> TCGA-08-0518-01A-01 3 0.1501 0.862 0.000 0.000 0.924 0.076 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.1444 0.864 0.000 0.000 0.928 0.072 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.1501 0.862 0.000 0.000 0.924 0.076 0.000 0.000
#> TCGA-02-0057-01A-01 6 0.4434 0.126 0.000 0.028 0.428 0.000 0.000 0.544
#> TCGA-02-0004-01A-01 5 0.0458 0.994 0.000 0.016 0.000 0.000 0.984 0.000
#> TCGA-02-0006-01B-01 2 0.0458 0.867 0.000 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0025-01A-01 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-02-0033-01A-01 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-02-0034-01A-01 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-02-0039-01A-01 2 0.1838 0.832 0.000 0.916 0.068 0.000 0.000 0.016
#> TCGA-02-0051-01A-01 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-02-0054-01A-01 2 0.1625 0.841 0.000 0.928 0.012 0.000 0.000 0.060
#> TCGA-02-0055-01A-01 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-02-0059-01A-01 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-02-0064-01A-01 2 0.0632 0.873 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-02-0075-01A-01 2 0.0632 0.873 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-02-0079-01A-03 2 0.0260 0.871 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-02-0085-01A-01 6 0.3090 0.646 0.004 0.028 0.000 0.140 0.000 0.828
#> TCGA-02-0086-01A-01 2 0.0632 0.873 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-02-0099-01A-01 2 0.0260 0.870 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-02-0106-01A-01 2 0.3782 0.267 0.000 0.588 0.000 0.000 0.412 0.000
#> TCGA-02-0107-01A-01 2 0.0632 0.873 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-02-0111-01A-01 2 0.0632 0.873 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-02-0326-01A-01 6 0.2547 0.638 0.004 0.016 0.112 0.000 0.000 0.868
#> TCGA-02-0337-01A-01 2 0.7197 -0.219 0.072 0.424 0.000 0.124 0.032 0.348
#> TCGA-06-0122-01A-01 2 0.2146 0.808 0.000 0.880 0.116 0.000 0.000 0.004
#> TCGA-06-0124-01A-01 2 0.0363 0.873 0.000 0.988 0.000 0.000 0.012 0.000
#> TCGA-06-0130-01A-01 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-06-0139-01A-01 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-06-0143-01A-01 2 0.1333 0.850 0.000 0.944 0.048 0.000 0.000 0.008
#> TCGA-06-0147-01A-01 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-06-0149-01A-05 2 0.4189 0.395 0.000 0.604 0.376 0.000 0.000 0.020
#> TCGA-06-0152-01A-02 3 0.3548 0.748 0.000 0.068 0.796 0.000 0.000 0.136
#> TCGA-06-0154-01A-02 2 0.0632 0.873 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-06-0164-01A-01 2 0.0713 0.871 0.000 0.972 0.000 0.000 0.028 0.000
#> TCGA-06-0175-01A-01 2 0.3017 0.783 0.000 0.844 0.084 0.000 0.000 0.072
#> TCGA-06-0176-01A-03 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-06-0184-01A-01 2 0.4669 0.609 0.000 0.688 0.148 0.000 0.000 0.164
#> TCGA-06-0189-01A-05 2 0.0713 0.871 0.000 0.972 0.000 0.000 0.028 0.000
#> TCGA-06-0190-01A-01 2 0.0713 0.871 0.000 0.972 0.000 0.000 0.028 0.000
#> TCGA-06-0194-01A-01 2 0.0632 0.873 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-06-0197-01A-02 2 0.2854 0.691 0.000 0.792 0.000 0.000 0.208 0.000
#> TCGA-06-0210-01A-01 2 0.0260 0.870 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-06-0397-01A-01 2 0.0632 0.873 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-06-0409-01A-02 2 0.0458 0.873 0.000 0.984 0.000 0.000 0.016 0.000
#> TCGA-06-0412-01A-01 2 0.3819 0.498 0.000 0.652 0.340 0.000 0.000 0.008
#> TCGA-06-0644-01A-02 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-06-0645-01A-01 2 0.0146 0.871 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-08-0346-01A-01 2 0.0146 0.871 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-08-0352-01A-01 2 0.3053 0.736 0.000 0.812 0.168 0.000 0.000 0.020
#> TCGA-08-0360-01A-01 2 0.0632 0.873 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-08-0390-01A-01 2 0.0632 0.865 0.000 0.976 0.000 0.000 0.000 0.024
#> TCGA-08-0392-01A-01 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-08-0509-01A-01 2 0.0260 0.870 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-08-0510-01A-01 2 0.3934 0.420 0.000 0.616 0.376 0.000 0.000 0.008
#> TCGA-08-0512-01A-01 2 0.0790 0.869 0.000 0.968 0.000 0.000 0.032 0.000
#> TCGA-08-0522-01A-01 5 0.0363 1.000 0.000 0.012 0.000 0.000 0.988 0.000
#> TCGA-12-0619-01A-01 2 0.0632 0.873 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-12-0620-01A-01 2 0.2357 0.796 0.000 0.872 0.116 0.000 0.000 0.012
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> SD:mclust 166 2.09e-32 2
#> SD:mclust 134 1.60e-52 3
#> SD:mclust 140 8.88e-57 4
#> SD:mclust 164 1.22e-55 5
#> SD:mclust 146 1.89e-60 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "NMF"]
# you can also extract it by
# res = res_list["SD:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.860 0.920 0.966 0.4915 0.506 0.506
#> 3 3 0.624 0.702 0.813 0.3373 0.749 0.541
#> 4 4 0.945 0.928 0.969 0.1406 0.861 0.617
#> 5 5 0.796 0.692 0.838 0.0402 0.949 0.810
#> 6 6 0.748 0.679 0.815 0.0360 0.948 0.788
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.0938 0.944 0.988 0.012
#> TCGA-02-0048-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0084-01A-03 2 0.0672 0.966 0.008 0.992
#> TCGA-02-0087-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0104-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.9087 0.564 0.676 0.324
#> TCGA-02-0325-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.4815 0.867 0.896 0.104
#> TCGA-06-0128-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.7815 0.720 0.768 0.232
#> TCGA-06-0166-01A-01 1 0.5178 0.857 0.884 0.116
#> TCGA-06-0174-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0648-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0348-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0353-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0115-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.0376 0.970 0.004 0.996
#> TCGA-06-0133-01A-02 2 0.5946 0.814 0.144 0.856
#> TCGA-06-0138-01A-02 2 0.1184 0.959 0.016 0.984
#> TCGA-06-0160-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.0376 0.970 0.004 0.996
#> TCGA-06-0167-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0171-01A-02 1 0.9129 0.529 0.672 0.328
#> TCGA-06-0173-01A-01 2 0.0672 0.967 0.008 0.992
#> TCGA-06-0179-01A-02 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0185-01A-01 2 0.0376 0.970 0.004 0.996
#> TCGA-06-0195-01B-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.3431 0.911 0.064 0.936
#> TCGA-06-0214-01A-02 2 0.0672 0.966 0.008 0.992
#> TCGA-06-0219-01A-01 2 0.9248 0.473 0.340 0.660
#> TCGA-06-0221-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0237-01A-02 1 0.1414 0.939 0.980 0.020
#> TCGA-06-0240-01A-02 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0349-01A-01 1 0.9608 0.401 0.616 0.384
#> TCGA-08-0380-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0520-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0007-01A-01 1 0.6531 0.801 0.832 0.168
#> TCGA-02-0009-01A-01 1 0.9393 0.490 0.644 0.356
#> TCGA-02-0016-01A-01 1 0.0672 0.947 0.992 0.008
#> TCGA-02-0021-01A-01 2 0.8207 0.636 0.256 0.744
#> TCGA-02-0023-01B-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.8144 0.690 0.748 0.252
#> TCGA-02-0038-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0043-01A-01 2 0.9996 -0.022 0.488 0.512
#> TCGA-02-0070-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0102-01A-01 2 0.9170 0.477 0.332 0.668
#> TCGA-02-0260-01A-03 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0269-01B-01 1 0.0672 0.947 0.992 0.008
#> TCGA-02-0285-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0289-01A-01 1 0.7815 0.720 0.768 0.232
#> TCGA-02-0290-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0317-01A-01 1 0.8813 0.608 0.700 0.300
#> TCGA-02-0333-01A-02 1 0.7815 0.720 0.768 0.232
#> TCGA-02-0422-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0430-01A-01 2 0.8813 0.549 0.300 0.700
#> TCGA-06-0125-01A-01 1 0.7299 0.758 0.796 0.204
#> TCGA-06-0126-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0137-01A-03 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0145-01A-04 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0148-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0187-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0211-01B-01 1 0.1414 0.938 0.980 0.020
#> TCGA-06-0402-01A-01 2 0.4161 0.887 0.084 0.916
#> TCGA-08-0246-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0357-01A-01 2 0.9608 0.343 0.384 0.616
#> TCGA-08-0358-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0375-01A-01 1 0.5408 0.849 0.876 0.124
#> TCGA-08-0511-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0514-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0529-01A-02 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0531-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0057-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-02-0337-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0147-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.973 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.973 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.973 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0747 0.773 0.984 0.000 0.016
#> TCGA-02-0010-01A-01 1 0.2625 0.731 0.916 0.000 0.084
#> TCGA-02-0011-01B-01 1 0.3340 0.772 0.880 0.000 0.120
#> TCGA-02-0014-01A-01 1 0.2066 0.751 0.940 0.000 0.060
#> TCGA-02-0024-01B-01 1 0.1529 0.762 0.960 0.000 0.040
#> TCGA-02-0026-01B-01 1 0.1529 0.762 0.960 0.000 0.040
#> TCGA-02-0028-01A-01 1 0.4291 0.601 0.820 0.000 0.180
#> TCGA-02-0046-01A-01 1 0.4121 0.621 0.832 0.000 0.168
#> TCGA-02-0047-01A-01 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-02-0048-01A-01 3 0.6095 0.590 0.392 0.000 0.608
#> TCGA-02-0060-01A-01 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-02-0069-01A-01 1 0.2625 0.731 0.916 0.000 0.084
#> TCGA-02-0074-01A-01 1 0.1411 0.763 0.964 0.000 0.036
#> TCGA-02-0080-01A-01 1 0.3879 0.764 0.848 0.000 0.152
#> TCGA-02-0084-01A-03 2 0.8322 0.521 0.120 0.604 0.276
#> TCGA-02-0087-01A-01 1 0.5859 0.706 0.656 0.000 0.344
#> TCGA-02-0104-01A-01 1 0.2066 0.779 0.940 0.000 0.060
#> TCGA-02-0114-01A-01 1 0.2066 0.751 0.940 0.000 0.060
#> TCGA-02-0281-01A-01 1 0.3619 0.670 0.864 0.000 0.136
#> TCGA-02-0321-01A-01 1 0.5554 0.627 0.812 0.112 0.076
#> TCGA-02-0325-01A-01 1 0.3412 0.675 0.876 0.000 0.124
#> TCGA-02-0338-01A-01 1 0.2537 0.735 0.920 0.000 0.080
#> TCGA-02-0339-01A-01 1 0.2066 0.751 0.940 0.000 0.060
#> TCGA-02-0432-01A-02 1 0.5835 0.708 0.660 0.000 0.340
#> TCGA-02-0439-01A-01 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-02-0440-01A-01 1 0.1163 0.767 0.972 0.000 0.028
#> TCGA-02-0446-01A-01 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-06-0128-01A-01 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-06-0129-01A-01 1 0.2066 0.779 0.940 0.000 0.060
#> TCGA-06-0146-01A-01 1 0.3116 0.776 0.892 0.000 0.108
#> TCGA-06-0156-01A-01 1 0.6848 0.705 0.736 0.100 0.164
#> TCGA-06-0166-01A-01 1 0.4369 0.762 0.864 0.040 0.096
#> TCGA-06-0174-01A-01 1 0.2066 0.751 0.940 0.000 0.060
#> TCGA-06-0177-01A-01 1 0.1289 0.778 0.968 0.000 0.032
#> TCGA-06-0238-01A-02 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-06-0241-01A-02 1 0.1964 0.768 0.944 0.000 0.056
#> TCGA-06-0410-01A-01 1 0.2796 0.771 0.908 0.000 0.092
#> TCGA-06-0413-01A-01 1 0.2625 0.731 0.916 0.000 0.084
#> TCGA-06-0414-01A-01 1 0.2878 0.776 0.904 0.000 0.096
#> TCGA-06-0646-01A-01 2 0.0424 0.878 0.008 0.992 0.000
#> TCGA-06-0648-01A-01 1 0.1529 0.779 0.960 0.000 0.040
#> TCGA-08-0245-01A-01 1 0.2537 0.735 0.920 0.000 0.080
#> TCGA-08-0344-01A-01 1 0.0892 0.769 0.980 0.000 0.020
#> TCGA-08-0347-01A-01 1 0.5785 0.711 0.668 0.000 0.332
#> TCGA-08-0348-01A-01 1 0.4605 0.751 0.796 0.000 0.204
#> TCGA-08-0350-01A-01 1 0.1031 0.776 0.976 0.000 0.024
#> TCGA-08-0353-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-08-0359-01A-01 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-08-0385-01A-01 1 0.1529 0.762 0.960 0.000 0.040
#> TCGA-08-0517-01A-01 1 0.2356 0.742 0.928 0.000 0.072
#> TCGA-08-0524-01A-01 1 0.2356 0.742 0.928 0.000 0.072
#> TCGA-12-0616-01A-01 1 0.1964 0.753 0.944 0.000 0.056
#> TCGA-12-0618-01A-01 1 0.0237 0.773 0.996 0.000 0.004
#> TCGA-02-0089-01A-01 2 0.2711 0.820 0.000 0.912 0.088
#> TCGA-02-0113-01A-01 3 0.6308 0.349 0.000 0.492 0.508
#> TCGA-02-0115-01A-01 2 0.7551 0.505 0.048 0.580 0.372
#> TCGA-02-0451-01A-01 2 0.5873 0.608 0.004 0.684 0.312
#> TCGA-06-0132-01A-02 2 0.8425 0.454 0.100 0.552 0.348
#> TCGA-06-0133-01A-02 3 0.9992 -0.305 0.320 0.328 0.352
#> TCGA-06-0138-01A-02 2 0.9343 0.284 0.176 0.476 0.348
#> TCGA-06-0160-01A-01 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-06-0162-01A-01 2 0.8546 0.440 0.108 0.544 0.348
#> TCGA-06-0167-01A-01 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-06-0171-01A-02 1 0.6104 0.702 0.648 0.004 0.348
#> TCGA-06-0173-01A-01 2 0.4802 0.744 0.020 0.824 0.156
#> TCGA-06-0179-01A-02 2 0.8230 0.475 0.088 0.564 0.348
#> TCGA-06-0182-01A-01 3 0.6518 0.305 0.004 0.484 0.512
#> TCGA-06-0185-01A-01 3 0.4840 0.453 0.016 0.168 0.816
#> TCGA-06-0195-01B-01 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-06-0208-01B-01 3 0.5955 0.329 0.048 0.180 0.772
#> TCGA-06-0214-01A-02 2 0.6800 0.587 0.032 0.660 0.308
#> TCGA-06-0219-01A-01 1 0.7150 0.676 0.616 0.036 0.348
#> TCGA-06-0221-01A-01 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-06-0237-01A-02 1 0.6235 0.639 0.564 0.000 0.436
#> TCGA-06-0240-01A-02 1 0.5882 0.705 0.652 0.000 0.348
#> TCGA-08-0349-01A-01 1 0.7251 0.674 0.612 0.040 0.348
#> TCGA-08-0380-01A-01 2 0.7023 0.548 0.032 0.624 0.344
#> TCGA-08-0386-01A-01 3 0.5926 0.640 0.356 0.000 0.644
#> TCGA-08-0520-01A-01 2 0.6659 0.428 0.008 0.532 0.460
#> TCGA-02-0007-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-02-0009-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-02-0016-01A-01 3 0.5835 0.648 0.340 0.000 0.660
#> TCGA-02-0021-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-02-0023-01B-01 3 0.6252 0.427 0.000 0.444 0.556
#> TCGA-02-0027-01A-01 3 0.5905 0.646 0.352 0.000 0.648
#> TCGA-02-0038-01A-01 3 0.6302 0.374 0.000 0.480 0.520
#> TCGA-02-0043-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-02-0070-01A-01 3 0.6750 0.574 0.024 0.336 0.640
#> TCGA-02-0102-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-02-0260-01A-03 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-02-0269-01B-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-02-0285-01A-01 3 0.6126 0.503 0.000 0.400 0.600
#> TCGA-02-0289-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-02-0290-01A-01 3 0.6204 0.468 0.000 0.424 0.576
#> TCGA-02-0317-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-02-0333-01A-02 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-02-0422-01A-01 3 0.8077 0.664 0.176 0.172 0.652
#> TCGA-02-0430-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-06-0125-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-06-0126-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-06-0137-01A-03 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-06-0145-01A-04 3 0.6189 0.545 0.004 0.364 0.632
#> TCGA-06-0148-01A-01 3 0.6717 0.559 0.020 0.352 0.628
#> TCGA-06-0187-01A-01 3 0.6140 0.497 0.000 0.404 0.596
#> TCGA-06-0211-01B-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-06-0402-01A-01 3 0.6081 0.651 0.344 0.004 0.652
#> TCGA-08-0246-01A-01 3 0.6305 0.366 0.000 0.484 0.516
#> TCGA-08-0354-01A-01 3 0.6305 0.367 0.000 0.484 0.516
#> TCGA-08-0355-01A-01 3 0.6295 0.389 0.000 0.472 0.528
#> TCGA-08-0357-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-08-0358-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-08-0375-01A-01 3 0.5882 0.651 0.348 0.000 0.652
#> TCGA-08-0511-01A-01 3 0.6126 0.503 0.000 0.400 0.600
#> TCGA-08-0514-01A-01 3 0.6180 0.480 0.000 0.416 0.584
#> TCGA-08-0518-01A-01 3 0.8072 0.664 0.164 0.184 0.652
#> TCGA-08-0529-01A-02 3 0.7545 0.626 0.076 0.272 0.652
#> TCGA-08-0531-01A-01 3 0.8067 0.664 0.188 0.160 0.652
#> TCGA-02-0057-01A-01 2 0.1964 0.845 0.000 0.944 0.056
#> TCGA-02-0004-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0054-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0075-01A-01 2 0.0892 0.869 0.000 0.980 0.020
#> TCGA-02-0079-01A-03 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0085-01A-01 2 0.6448 0.581 0.016 0.656 0.328
#> TCGA-02-0086-01A-01 2 0.0237 0.882 0.000 0.996 0.004
#> TCGA-02-0099-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0106-01A-01 2 0.0237 0.882 0.000 0.996 0.004
#> TCGA-02-0107-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-02-0326-01A-01 2 0.7095 0.590 0.048 0.660 0.292
#> TCGA-02-0337-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0122-01A-01 2 0.4605 0.608 0.000 0.796 0.204
#> TCGA-06-0124-01A-01 2 0.0592 0.875 0.000 0.988 0.012
#> TCGA-06-0130-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0143-01A-01 2 0.3551 0.735 0.000 0.868 0.132
#> TCGA-06-0147-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 2 0.0592 0.875 0.000 0.988 0.012
#> TCGA-06-0152-01A-02 3 0.6309 0.337 0.000 0.496 0.504
#> TCGA-06-0154-01A-02 2 0.2356 0.810 0.000 0.928 0.072
#> TCGA-06-0164-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0210-01A-01 2 0.0237 0.882 0.000 0.996 0.004
#> TCGA-06-0397-01A-01 2 0.0424 0.879 0.000 0.992 0.008
#> TCGA-06-0409-01A-02 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0412-01A-01 3 0.6309 0.337 0.000 0.496 0.504
#> TCGA-06-0644-01A-02 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-08-0352-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.0237 0.882 0.000 0.996 0.004
#> TCGA-08-0392-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 2 0.5560 0.357 0.000 0.700 0.300
#> TCGA-08-0512-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.884 0.000 1.000 0.000
#> TCGA-12-0620-01A-01 2 0.2261 0.816 0.000 0.932 0.068
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.0336 0.977 0.992 0.000 0.000 0.008
#> TCGA-02-0010-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0817 0.965 0.976 0.000 0.000 0.024
#> TCGA-02-0014-01A-01 1 0.0188 0.978 0.996 0.000 0.000 0.004
#> TCGA-02-0024-01B-01 1 0.0188 0.978 0.996 0.000 0.000 0.004
#> TCGA-02-0026-01B-01 1 0.0188 0.978 0.996 0.000 0.000 0.004
#> TCGA-02-0028-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 4 0.0188 0.951 0.004 0.000 0.000 0.996
#> TCGA-02-0048-01A-01 3 0.4103 0.660 0.256 0.000 0.744 0.000
#> TCGA-02-0060-01A-01 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-02-0069-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0188 0.978 0.996 0.000 0.000 0.004
#> TCGA-02-0080-01A-01 4 0.4661 0.470 0.348 0.000 0.000 0.652
#> TCGA-02-0084-01A-03 4 0.0779 0.944 0.000 0.004 0.016 0.980
#> TCGA-02-0087-01A-01 4 0.0188 0.951 0.004 0.000 0.000 0.996
#> TCGA-02-0104-01A-01 1 0.0336 0.977 0.992 0.000 0.000 0.008
#> TCGA-02-0114-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.0188 0.975 0.996 0.004 0.000 0.000
#> TCGA-02-0325-01A-01 1 0.2859 0.856 0.880 0.000 0.112 0.008
#> TCGA-02-0338-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0188 0.978 0.996 0.000 0.000 0.004
#> TCGA-02-0432-01A-02 4 0.2149 0.879 0.088 0.000 0.000 0.912
#> TCGA-02-0439-01A-01 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-02-0440-01A-01 1 0.0188 0.978 0.996 0.000 0.000 0.004
#> TCGA-02-0446-01A-01 1 0.4866 0.301 0.596 0.000 0.000 0.404
#> TCGA-06-0128-01A-01 4 0.4277 0.616 0.280 0.000 0.000 0.720
#> TCGA-06-0129-01A-01 1 0.0469 0.974 0.988 0.000 0.000 0.012
#> TCGA-06-0146-01A-01 1 0.0707 0.968 0.980 0.000 0.000 0.020
#> TCGA-06-0156-01A-01 1 0.3142 0.831 0.860 0.132 0.000 0.008
#> TCGA-06-0166-01A-01 1 0.0188 0.978 0.996 0.000 0.000 0.004
#> TCGA-06-0174-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0188 0.978 0.996 0.000 0.000 0.004
#> TCGA-06-0238-01A-02 4 0.0188 0.951 0.004 0.000 0.000 0.996
#> TCGA-06-0241-01A-02 1 0.0188 0.978 0.996 0.000 0.000 0.004
#> TCGA-06-0410-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0336 0.977 0.992 0.000 0.000 0.008
#> TCGA-06-0646-01A-01 2 0.0336 0.960 0.008 0.992 0.000 0.000
#> TCGA-06-0648-01A-01 1 0.0336 0.977 0.992 0.000 0.000 0.008
#> TCGA-08-0245-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0336 0.977 0.992 0.000 0.000 0.008
#> TCGA-08-0347-01A-01 4 0.1022 0.932 0.032 0.000 0.000 0.968
#> TCGA-08-0348-01A-01 1 0.0592 0.971 0.984 0.000 0.000 0.016
#> TCGA-08-0350-01A-01 1 0.0188 0.978 0.996 0.000 0.000 0.004
#> TCGA-08-0353-01A-01 3 0.1716 0.916 0.064 0.000 0.936 0.000
#> TCGA-08-0359-01A-01 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-08-0385-01A-01 1 0.0188 0.978 0.996 0.000 0.000 0.004
#> TCGA-08-0517-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.978 1.000 0.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0336 0.977 0.992 0.000 0.000 0.008
#> TCGA-02-0089-01A-01 4 0.0895 0.942 0.000 0.004 0.020 0.976
#> TCGA-02-0113-01A-01 3 0.0592 0.955 0.000 0.000 0.984 0.016
#> TCGA-02-0115-01A-01 4 0.0336 0.949 0.000 0.000 0.008 0.992
#> TCGA-02-0451-01A-01 4 0.0336 0.949 0.000 0.008 0.000 0.992
#> TCGA-06-0132-01A-02 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-06-0133-01A-02 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 4 0.0188 0.951 0.000 0.004 0.000 0.996
#> TCGA-06-0160-01A-01 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-06-0162-01A-01 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-06-0171-01A-02 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 4 0.2149 0.880 0.000 0.088 0.000 0.912
#> TCGA-06-0179-01A-02 4 0.0188 0.951 0.000 0.004 0.000 0.996
#> TCGA-06-0182-01A-01 3 0.4956 0.716 0.000 0.056 0.756 0.188
#> TCGA-06-0185-01A-01 3 0.4477 0.554 0.000 0.000 0.688 0.312
#> TCGA-06-0195-01B-01 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-06-0208-01B-01 4 0.4103 0.646 0.000 0.000 0.256 0.744
#> TCGA-06-0214-01A-02 4 0.0336 0.949 0.000 0.008 0.000 0.992
#> TCGA-06-0219-01A-01 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 4 0.0188 0.951 0.000 0.000 0.004 0.996
#> TCGA-06-0240-01A-02 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-08-0349-01A-01 4 0.0000 0.952 0.000 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 4 0.0336 0.949 0.000 0.008 0.000 0.992
#> TCGA-08-0386-01A-01 3 0.2760 0.841 0.000 0.000 0.872 0.128
#> TCGA-08-0520-01A-01 4 0.0336 0.949 0.000 0.000 0.008 0.992
#> TCGA-02-0007-01A-01 3 0.1118 0.940 0.036 0.000 0.964 0.000
#> TCGA-02-0009-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0016-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0021-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0027-01A-01 3 0.0188 0.964 0.004 0.000 0.996 0.000
#> TCGA-02-0038-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0043-01A-01 3 0.0921 0.947 0.028 0.000 0.972 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0260-01A-03 3 0.0188 0.964 0.004 0.000 0.996 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-06-0137-01A-03 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-06-0402-01A-01 3 0.0188 0.964 0.004 0.000 0.996 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-08-0354-01A-01 3 0.1022 0.940 0.000 0.032 0.968 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-08-0357-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-08-0358-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-08-0375-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-02-0057-01A-01 4 0.3402 0.799 0.000 0.004 0.164 0.832
#> TCGA-02-0004-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0707 0.950 0.000 0.980 0.000 0.020
#> TCGA-02-0051-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0079-01A-03 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0085-01A-01 4 0.0336 0.949 0.000 0.008 0.000 0.992
#> TCGA-02-0086-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0106-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-02-0326-01A-01 4 0.3610 0.752 0.000 0.000 0.200 0.800
#> TCGA-02-0337-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0122-01A-01 2 0.4981 0.153 0.000 0.536 0.464 0.000
#> TCGA-06-0124-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 2 0.0469 0.957 0.000 0.988 0.012 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.4356 0.595 0.000 0.708 0.292 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.966 0.000 0.000 1.000 0.000
#> TCGA-06-0154-01A-02 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.4564 0.498 0.000 0.672 0.000 0.328
#> TCGA-06-0189-01A-05 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 3 0.3801 0.716 0.000 0.220 0.780 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-08-0352-01A-01 2 0.4585 0.514 0.000 0.668 0.332 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.0817 0.947 0.000 0.976 0.000 0.024
#> TCGA-08-0392-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.2647 0.848 0.000 0.120 0.880 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.2011 0.890 0.000 0.920 0.080 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.2669 0.8102 0.876 0.000 0.000 0.020 0.104
#> TCGA-02-0010-01A-01 1 0.0324 0.8331 0.992 0.000 0.000 0.004 0.004
#> TCGA-02-0011-01B-01 1 0.3774 0.5835 0.704 0.000 0.000 0.000 0.296
#> TCGA-02-0014-01A-01 1 0.1544 0.8276 0.932 0.000 0.000 0.000 0.068
#> TCGA-02-0024-01B-01 1 0.0771 0.8335 0.976 0.000 0.000 0.004 0.020
#> TCGA-02-0026-01B-01 1 0.1041 0.8278 0.964 0.000 0.000 0.004 0.032
#> TCGA-02-0028-01A-01 1 0.2439 0.8124 0.876 0.000 0.000 0.004 0.120
#> TCGA-02-0046-01A-01 1 0.1443 0.8314 0.948 0.000 0.004 0.004 0.044
#> TCGA-02-0047-01A-01 1 0.6645 -0.2910 0.400 0.000 0.000 0.224 0.376
#> TCGA-02-0048-01A-01 3 0.5052 0.2675 0.412 0.000 0.552 0.000 0.036
#> TCGA-02-0060-01A-01 5 0.5638 0.5732 0.152 0.000 0.000 0.216 0.632
#> TCGA-02-0069-01A-01 1 0.0162 0.8329 0.996 0.000 0.000 0.004 0.000
#> TCGA-02-0074-01A-01 1 0.1357 0.8234 0.948 0.000 0.000 0.004 0.048
#> TCGA-02-0080-01A-01 1 0.6210 -0.1189 0.456 0.000 0.000 0.140 0.404
#> TCGA-02-0084-01A-03 4 0.7348 -0.2897 0.148 0.048 0.004 0.420 0.380
#> TCGA-02-0087-01A-01 4 0.6494 -0.3038 0.164 0.004 0.000 0.452 0.380
#> TCGA-02-0104-01A-01 1 0.2605 0.7982 0.852 0.000 0.000 0.000 0.148
#> TCGA-02-0114-01A-01 1 0.2230 0.8134 0.884 0.000 0.000 0.000 0.116
#> TCGA-02-0281-01A-01 1 0.1952 0.8253 0.912 0.000 0.000 0.004 0.084
#> TCGA-02-0321-01A-01 1 0.3209 0.7333 0.848 0.120 0.000 0.004 0.028
#> TCGA-02-0325-01A-01 1 0.6050 0.3961 0.580 0.000 0.148 0.004 0.268
#> TCGA-02-0338-01A-01 1 0.2074 0.8190 0.896 0.000 0.000 0.000 0.104
#> TCGA-02-0339-01A-01 1 0.0671 0.8319 0.980 0.000 0.000 0.004 0.016
#> TCGA-02-0432-01A-02 5 0.6287 0.4074 0.312 0.000 0.000 0.176 0.512
#> TCGA-02-0439-01A-01 4 0.6162 -0.3627 0.132 0.000 0.000 0.440 0.428
#> TCGA-02-0440-01A-01 1 0.0404 0.8314 0.988 0.000 0.000 0.000 0.012
#> TCGA-02-0446-01A-01 1 0.4672 0.6582 0.752 0.040 0.000 0.028 0.180
#> TCGA-06-0128-01A-01 1 0.6031 0.3092 0.576 0.000 0.000 0.180 0.244
#> TCGA-06-0129-01A-01 1 0.1571 0.8185 0.936 0.000 0.000 0.004 0.060
#> TCGA-06-0146-01A-01 1 0.3876 0.5542 0.684 0.000 0.000 0.000 0.316
#> TCGA-06-0156-01A-01 1 0.1310 0.8292 0.956 0.024 0.000 0.000 0.020
#> TCGA-06-0166-01A-01 1 0.2278 0.8190 0.908 0.032 0.000 0.000 0.060
#> TCGA-06-0174-01A-01 1 0.2471 0.8039 0.864 0.000 0.000 0.000 0.136
#> TCGA-06-0177-01A-01 1 0.0794 0.8287 0.972 0.000 0.000 0.000 0.028
#> TCGA-06-0238-01A-02 4 0.6422 -0.2111 0.308 0.000 0.000 0.492 0.200
#> TCGA-06-0241-01A-02 1 0.2424 0.8075 0.868 0.000 0.000 0.000 0.132
#> TCGA-06-0410-01A-01 1 0.3003 0.7736 0.812 0.000 0.000 0.000 0.188
#> TCGA-06-0413-01A-01 1 0.0566 0.8325 0.984 0.000 0.000 0.004 0.012
#> TCGA-06-0414-01A-01 1 0.1043 0.8325 0.960 0.000 0.000 0.000 0.040
#> TCGA-06-0646-01A-01 2 0.5854 0.5009 0.092 0.596 0.000 0.300 0.012
#> TCGA-06-0648-01A-01 1 0.1608 0.8112 0.928 0.000 0.000 0.000 0.072
#> TCGA-08-0245-01A-01 1 0.2516 0.8022 0.860 0.000 0.000 0.000 0.140
#> TCGA-08-0344-01A-01 1 0.1121 0.8244 0.956 0.000 0.000 0.000 0.044
#> TCGA-08-0347-01A-01 1 0.6330 -0.0999 0.456 0.000 0.000 0.160 0.384
#> TCGA-08-0348-01A-01 1 0.3336 0.6770 0.772 0.000 0.000 0.000 0.228
#> TCGA-08-0350-01A-01 1 0.3143 0.7077 0.796 0.000 0.000 0.000 0.204
#> TCGA-08-0353-01A-01 3 0.2389 0.8302 0.116 0.000 0.880 0.004 0.000
#> TCGA-08-0359-01A-01 5 0.5464 0.5740 0.128 0.000 0.000 0.224 0.648
#> TCGA-08-0385-01A-01 1 0.1357 0.8226 0.948 0.000 0.000 0.004 0.048
#> TCGA-08-0517-01A-01 1 0.2230 0.8146 0.884 0.000 0.000 0.000 0.116
#> TCGA-08-0524-01A-01 1 0.2377 0.8087 0.872 0.000 0.000 0.000 0.128
#> TCGA-12-0616-01A-01 1 0.2690 0.7938 0.844 0.000 0.000 0.000 0.156
#> TCGA-12-0618-01A-01 1 0.0880 0.8279 0.968 0.000 0.000 0.000 0.032
#> TCGA-02-0089-01A-01 4 0.3282 0.3646 0.000 0.000 0.008 0.804 0.188
#> TCGA-02-0113-01A-01 4 0.6325 0.0670 0.000 0.000 0.420 0.424 0.156
#> TCGA-02-0115-01A-01 4 0.4403 -0.0596 0.000 0.000 0.004 0.560 0.436
#> TCGA-02-0451-01A-01 4 0.0865 0.4415 0.000 0.000 0.004 0.972 0.024
#> TCGA-06-0132-01A-02 5 0.4297 0.2439 0.000 0.000 0.000 0.472 0.528
#> TCGA-06-0133-01A-02 4 0.3715 0.3046 0.000 0.000 0.004 0.736 0.260
#> TCGA-06-0138-01A-02 4 0.0671 0.4439 0.004 0.000 0.000 0.980 0.016
#> TCGA-06-0160-01A-01 5 0.4425 0.4412 0.008 0.000 0.000 0.392 0.600
#> TCGA-06-0162-01A-01 4 0.1502 0.4448 0.000 0.000 0.004 0.940 0.056
#> TCGA-06-0167-01A-01 5 0.4201 0.4118 0.000 0.000 0.000 0.408 0.592
#> TCGA-06-0171-01A-02 4 0.1571 0.4512 0.004 0.000 0.000 0.936 0.060
#> TCGA-06-0173-01A-01 4 0.4295 0.4142 0.004 0.008 0.028 0.760 0.200
#> TCGA-06-0179-01A-02 4 0.4273 -0.1000 0.000 0.000 0.000 0.552 0.448
#> TCGA-06-0182-01A-01 4 0.6606 0.2596 0.000 0.004 0.344 0.460 0.192
#> TCGA-06-0185-01A-01 4 0.5873 0.2833 0.000 0.000 0.348 0.540 0.112
#> TCGA-06-0195-01B-01 4 0.4135 0.1914 0.004 0.000 0.000 0.656 0.340
#> TCGA-06-0208-01B-01 4 0.6054 0.2992 0.000 0.000 0.304 0.548 0.148
#> TCGA-06-0214-01A-02 4 0.1124 0.4364 0.000 0.000 0.004 0.960 0.036
#> TCGA-06-0219-01A-01 4 0.4390 0.2838 0.004 0.000 0.000 0.568 0.428
#> TCGA-06-0221-01A-01 4 0.4009 0.2205 0.004 0.000 0.000 0.684 0.312
#> TCGA-06-0237-01A-02 4 0.2068 0.4431 0.000 0.000 0.004 0.904 0.092
#> TCGA-06-0240-01A-02 4 0.4307 -0.2598 0.000 0.000 0.000 0.504 0.496
#> TCGA-08-0349-01A-01 4 0.1205 0.4394 0.000 0.000 0.004 0.956 0.040
#> TCGA-08-0380-01A-01 4 0.1908 0.3802 0.000 0.000 0.000 0.908 0.092
#> TCGA-08-0386-01A-01 3 0.5088 0.5330 0.000 0.000 0.668 0.252 0.080
#> TCGA-08-0520-01A-01 4 0.3807 0.3679 0.000 0.000 0.012 0.748 0.240
#> TCGA-02-0007-01A-01 3 0.4272 0.7747 0.020 0.000 0.796 0.124 0.060
#> TCGA-02-0009-01A-01 3 0.0000 0.9323 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.0162 0.9320 0.000 0.000 0.996 0.000 0.004
#> TCGA-02-0021-01A-01 3 0.0162 0.9322 0.000 0.000 0.996 0.004 0.000
#> TCGA-02-0023-01B-01 3 0.0162 0.9322 0.000 0.000 0.996 0.000 0.004
#> TCGA-02-0027-01A-01 3 0.3502 0.8110 0.028 0.016 0.848 0.004 0.104
#> TCGA-02-0038-01A-01 3 0.4465 0.6796 0.000 0.000 0.736 0.204 0.060
#> TCGA-02-0043-01A-01 3 0.0960 0.9223 0.016 0.000 0.972 0.004 0.008
#> TCGA-02-0070-01A-01 3 0.0324 0.9312 0.000 0.000 0.992 0.004 0.004
#> TCGA-02-0102-01A-01 3 0.0324 0.9312 0.000 0.000 0.992 0.004 0.004
#> TCGA-02-0260-01A-03 3 0.0486 0.9294 0.004 0.000 0.988 0.004 0.004
#> TCGA-02-0269-01B-01 3 0.0324 0.9312 0.000 0.000 0.992 0.004 0.004
#> TCGA-02-0285-01A-01 3 0.0000 0.9323 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0289-01A-01 3 0.0162 0.9320 0.000 0.000 0.996 0.000 0.004
#> TCGA-02-0290-01A-01 3 0.0290 0.9314 0.000 0.000 0.992 0.008 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.9323 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0333-01A-02 3 0.0324 0.9312 0.000 0.000 0.992 0.004 0.004
#> TCGA-02-0422-01A-01 3 0.0162 0.9322 0.000 0.000 0.996 0.004 0.000
#> TCGA-02-0430-01A-01 3 0.0451 0.9303 0.000 0.000 0.988 0.008 0.004
#> TCGA-06-0125-01A-01 3 0.0324 0.9312 0.000 0.000 0.992 0.004 0.004
#> TCGA-06-0126-01A-01 3 0.0324 0.9312 0.000 0.000 0.992 0.004 0.004
#> TCGA-06-0137-01A-03 3 0.0162 0.9320 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0145-01A-04 3 0.0162 0.9322 0.000 0.000 0.996 0.004 0.000
#> TCGA-06-0148-01A-01 3 0.0324 0.9312 0.000 0.000 0.992 0.004 0.004
#> TCGA-06-0187-01A-01 3 0.0510 0.9281 0.000 0.000 0.984 0.016 0.000
#> TCGA-06-0211-01B-01 3 0.4022 0.7734 0.000 0.000 0.796 0.104 0.100
#> TCGA-06-0402-01A-01 3 0.2813 0.8591 0.004 0.000 0.880 0.032 0.084
#> TCGA-08-0246-01A-01 3 0.0404 0.9301 0.000 0.000 0.988 0.012 0.000
#> TCGA-08-0354-01A-01 3 0.5301 0.6064 0.000 0.000 0.676 0.176 0.148
#> TCGA-08-0355-01A-01 3 0.0703 0.9215 0.000 0.000 0.976 0.024 0.000
#> TCGA-08-0357-01A-01 3 0.0162 0.9322 0.000 0.000 0.996 0.004 0.000
#> TCGA-08-0358-01A-01 3 0.0324 0.9317 0.000 0.000 0.992 0.004 0.004
#> TCGA-08-0375-01A-01 3 0.0162 0.9318 0.000 0.000 0.996 0.004 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.9323 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0514-01A-01 3 0.0162 0.9322 0.000 0.000 0.996 0.004 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.9323 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.0162 0.9322 0.000 0.000 0.996 0.004 0.000
#> TCGA-08-0531-01A-01 3 0.0290 0.9314 0.000 0.000 0.992 0.008 0.000
#> TCGA-02-0057-01A-01 4 0.6829 -0.1323 0.000 0.088 0.064 0.512 0.336
#> TCGA-02-0004-01A-01 2 0.0162 0.9214 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0006-01B-01 2 0.2971 0.8160 0.000 0.836 0.000 0.156 0.008
#> TCGA-02-0025-01A-01 2 0.0000 0.9214 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0162 0.9214 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0034-01A-01 2 0.0000 0.9214 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0703 0.9159 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0051-01A-01 2 0.1410 0.8965 0.000 0.940 0.000 0.000 0.060
#> TCGA-02-0054-01A-01 2 0.5452 0.2331 0.000 0.492 0.000 0.448 0.060
#> TCGA-02-0055-01A-01 2 0.0290 0.9208 0.000 0.992 0.000 0.000 0.008
#> TCGA-02-0059-01A-01 2 0.0162 0.9214 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0064-01A-01 2 0.0865 0.9137 0.000 0.972 0.000 0.024 0.004
#> TCGA-02-0075-01A-01 2 0.0000 0.9214 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0079-01A-03 2 0.1997 0.8927 0.000 0.924 0.000 0.036 0.040
#> TCGA-02-0085-01A-01 5 0.6234 0.2306 0.000 0.304 0.000 0.172 0.524
#> TCGA-02-0086-01A-01 2 0.1697 0.8899 0.000 0.932 0.000 0.008 0.060
#> TCGA-02-0099-01A-01 2 0.0000 0.9214 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0106-01A-01 2 0.2286 0.8578 0.000 0.888 0.000 0.004 0.108
#> TCGA-02-0107-01A-01 2 0.0955 0.9119 0.000 0.968 0.000 0.028 0.004
#> TCGA-02-0111-01A-01 2 0.0162 0.9207 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0326-01A-01 5 0.6883 0.5105 0.132 0.028 0.076 0.124 0.640
#> TCGA-02-0337-01A-01 2 0.1872 0.8932 0.000 0.928 0.000 0.020 0.052
#> TCGA-06-0122-01A-01 2 0.5698 0.6054 0.000 0.668 0.196 0.116 0.020
#> TCGA-06-0124-01A-01 2 0.0000 0.9214 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0162 0.9214 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0139-01A-01 2 0.0162 0.9210 0.000 0.996 0.000 0.004 0.000
#> TCGA-06-0143-01A-01 2 0.2616 0.8695 0.000 0.888 0.000 0.076 0.036
#> TCGA-06-0147-01A-01 2 0.0324 0.9200 0.000 0.992 0.000 0.004 0.004
#> TCGA-06-0149-01A-05 2 0.6546 0.2733 0.000 0.488 0.148 0.352 0.012
#> TCGA-06-0152-01A-02 3 0.2773 0.7776 0.000 0.000 0.836 0.164 0.000
#> TCGA-06-0154-01A-02 2 0.0162 0.9210 0.000 0.996 0.004 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9214 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.1168 0.9038 0.000 0.960 0.032 0.000 0.008
#> TCGA-06-0176-01A-03 2 0.0404 0.9197 0.000 0.988 0.000 0.000 0.012
#> TCGA-06-0184-01A-01 4 0.4594 0.1487 0.000 0.360 0.008 0.624 0.008
#> TCGA-06-0189-01A-05 2 0.0162 0.9214 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0190-01A-01 2 0.0162 0.9214 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0194-01A-01 2 0.0162 0.9214 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0197-01A-02 2 0.0162 0.9214 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0210-01A-01 2 0.0000 0.9214 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0290 0.9207 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0409-01A-02 2 0.1502 0.8982 0.000 0.940 0.000 0.056 0.004
#> TCGA-06-0412-01A-01 3 0.2341 0.8757 0.000 0.056 0.912 0.012 0.020
#> TCGA-06-0644-01A-02 2 0.0404 0.9197 0.000 0.988 0.000 0.000 0.012
#> TCGA-06-0645-01A-01 2 0.2612 0.8465 0.000 0.868 0.000 0.124 0.008
#> TCGA-08-0346-01A-01 2 0.0000 0.9214 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0352-01A-01 2 0.1106 0.9090 0.000 0.964 0.024 0.000 0.012
#> TCGA-08-0360-01A-01 2 0.1894 0.8863 0.000 0.920 0.000 0.072 0.008
#> TCGA-08-0390-01A-01 2 0.4054 0.6095 0.000 0.732 0.000 0.248 0.020
#> TCGA-08-0392-01A-01 2 0.2971 0.8092 0.000 0.836 0.000 0.008 0.156
#> TCGA-08-0509-01A-01 2 0.2338 0.8595 0.000 0.884 0.000 0.112 0.004
#> TCGA-08-0510-01A-01 3 0.1662 0.8830 0.000 0.056 0.936 0.004 0.004
#> TCGA-08-0512-01A-01 2 0.0000 0.9214 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0162 0.9214 0.000 0.996 0.000 0.000 0.004
#> TCGA-12-0619-01A-01 2 0.0162 0.9214 0.000 0.996 0.000 0.000 0.004
#> TCGA-12-0620-01A-01 2 0.4799 0.5783 0.000 0.692 0.260 0.040 0.008
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.3305 0.7137 0.832 0.000 0.000 0.012 0.108 0.048
#> TCGA-02-0010-01A-01 1 0.0632 0.7564 0.976 0.000 0.000 0.000 0.024 0.000
#> TCGA-02-0011-01B-01 1 0.4550 0.4012 0.676 0.000 0.000 0.000 0.240 0.084
#> TCGA-02-0014-01A-01 1 0.1124 0.7621 0.956 0.000 0.000 0.000 0.036 0.008
#> TCGA-02-0024-01B-01 1 0.2509 0.7562 0.876 0.000 0.000 0.000 0.088 0.036
#> TCGA-02-0026-01B-01 1 0.2190 0.7234 0.900 0.000 0.000 0.000 0.060 0.040
#> TCGA-02-0028-01A-01 1 0.2002 0.7578 0.908 0.000 0.004 0.000 0.076 0.012
#> TCGA-02-0046-01A-01 1 0.2094 0.7542 0.908 0.000 0.016 0.000 0.068 0.008
#> TCGA-02-0047-01A-01 5 0.6517 0.5531 0.340 0.004 0.000 0.028 0.436 0.192
#> TCGA-02-0048-01A-01 1 0.5784 0.0733 0.480 0.000 0.420 0.056 0.036 0.008
#> TCGA-02-0060-01A-01 6 0.2103 0.6035 0.056 0.000 0.000 0.012 0.020 0.912
#> TCGA-02-0069-01A-01 1 0.1074 0.7560 0.960 0.000 0.000 0.000 0.028 0.012
#> TCGA-02-0074-01A-01 1 0.2882 0.6185 0.812 0.000 0.000 0.000 0.180 0.008
#> TCGA-02-0080-01A-01 1 0.6405 -0.4184 0.404 0.000 0.012 0.004 0.348 0.232
#> TCGA-02-0084-01A-03 5 0.6399 0.6043 0.180 0.044 0.004 0.084 0.624 0.064
#> TCGA-02-0087-01A-01 5 0.6337 0.6309 0.232 0.004 0.004 0.072 0.576 0.112
#> TCGA-02-0104-01A-01 1 0.3312 0.6914 0.792 0.000 0.000 0.000 0.180 0.028
#> TCGA-02-0114-01A-01 1 0.1926 0.7558 0.912 0.000 0.000 0.000 0.068 0.020
#> TCGA-02-0281-01A-01 1 0.1434 0.7628 0.940 0.000 0.000 0.000 0.048 0.012
#> TCGA-02-0321-01A-01 1 0.7140 -0.1655 0.400 0.304 0.000 0.016 0.232 0.048
#> TCGA-02-0325-01A-01 5 0.6286 0.3474 0.408 0.000 0.080 0.004 0.444 0.064
#> TCGA-02-0338-01A-01 1 0.2473 0.7319 0.856 0.000 0.000 0.000 0.136 0.008
#> TCGA-02-0339-01A-01 1 0.1794 0.7455 0.924 0.000 0.000 0.000 0.036 0.040
#> TCGA-02-0432-01A-02 6 0.6243 -0.4528 0.320 0.000 0.000 0.004 0.316 0.360
#> TCGA-02-0439-01A-01 5 0.6613 0.5064 0.200 0.000 0.004 0.048 0.496 0.252
#> TCGA-02-0440-01A-01 1 0.0692 0.7567 0.976 0.000 0.000 0.000 0.020 0.004
#> TCGA-02-0446-01A-01 1 0.4572 0.5864 0.752 0.088 0.000 0.000 0.048 0.112
#> TCGA-06-0128-01A-01 1 0.5717 -0.0500 0.540 0.000 0.000 0.076 0.344 0.040
#> TCGA-06-0129-01A-01 1 0.3404 0.5440 0.760 0.000 0.000 0.000 0.224 0.016
#> TCGA-06-0146-01A-01 1 0.4736 0.2464 0.620 0.000 0.000 0.000 0.308 0.072
#> TCGA-06-0156-01A-01 1 0.1863 0.7497 0.920 0.000 0.000 0.016 0.060 0.004
#> TCGA-06-0166-01A-01 1 0.3161 0.6889 0.848 0.092 0.000 0.000 0.040 0.020
#> TCGA-06-0174-01A-01 1 0.2869 0.7180 0.832 0.000 0.000 0.000 0.148 0.020
#> TCGA-06-0177-01A-01 1 0.1644 0.7555 0.932 0.000 0.000 0.000 0.040 0.028
#> TCGA-06-0238-01A-02 6 0.5713 0.3000 0.284 0.000 0.000 0.140 0.016 0.560
#> TCGA-06-0241-01A-02 1 0.2696 0.7330 0.856 0.000 0.000 0.000 0.116 0.028
#> TCGA-06-0410-01A-01 1 0.3866 0.6665 0.764 0.000 0.000 0.012 0.188 0.036
#> TCGA-06-0413-01A-01 1 0.1572 0.7534 0.936 0.000 0.000 0.000 0.028 0.036
#> TCGA-06-0414-01A-01 1 0.1333 0.7617 0.944 0.000 0.000 0.000 0.048 0.008
#> TCGA-06-0646-01A-01 5 0.7013 0.2501 0.120 0.112 0.000 0.300 0.460 0.008
#> TCGA-06-0648-01A-01 1 0.1865 0.7377 0.920 0.000 0.000 0.000 0.040 0.040
#> TCGA-08-0245-01A-01 1 0.3025 0.7104 0.820 0.000 0.000 0.000 0.156 0.024
#> TCGA-08-0344-01A-01 1 0.2070 0.7296 0.908 0.000 0.000 0.000 0.044 0.048
#> TCGA-08-0347-01A-01 5 0.5689 0.6003 0.316 0.004 0.000 0.000 0.520 0.160
#> TCGA-08-0348-01A-01 1 0.3884 0.4899 0.724 0.000 0.000 0.000 0.240 0.036
#> TCGA-08-0350-01A-01 1 0.4467 0.2775 0.632 0.000 0.000 0.000 0.320 0.048
#> TCGA-08-0353-01A-01 3 0.2398 0.8225 0.104 0.000 0.876 0.020 0.000 0.000
#> TCGA-08-0359-01A-01 6 0.4631 0.3340 0.092 0.000 0.000 0.008 0.200 0.700
#> TCGA-08-0385-01A-01 1 0.1863 0.7363 0.920 0.000 0.000 0.000 0.044 0.036
#> TCGA-08-0517-01A-01 1 0.1926 0.7586 0.912 0.000 0.000 0.000 0.068 0.020
#> TCGA-08-0524-01A-01 1 0.2613 0.7278 0.848 0.000 0.000 0.000 0.140 0.012
#> TCGA-12-0616-01A-01 1 0.3527 0.6939 0.792 0.000 0.000 0.004 0.164 0.040
#> TCGA-12-0618-01A-01 1 0.1649 0.7421 0.932 0.000 0.000 0.000 0.032 0.036
#> TCGA-02-0089-01A-01 4 0.5372 0.4782 0.000 0.004 0.012 0.628 0.120 0.236
#> TCGA-02-0113-01A-01 4 0.4045 0.5037 0.000 0.000 0.312 0.664 0.024 0.000
#> TCGA-02-0115-01A-01 6 0.2664 0.6507 0.000 0.000 0.000 0.184 0.000 0.816
#> TCGA-02-0451-01A-01 4 0.2365 0.6597 0.000 0.000 0.000 0.888 0.040 0.072
#> TCGA-06-0132-01A-02 6 0.2135 0.6856 0.000 0.000 0.000 0.128 0.000 0.872
#> TCGA-06-0133-01A-02 4 0.2964 0.5963 0.000 0.000 0.004 0.792 0.000 0.204
#> TCGA-06-0138-01A-02 4 0.1245 0.6784 0.000 0.000 0.000 0.952 0.032 0.016
#> TCGA-06-0160-01A-01 6 0.1863 0.6901 0.000 0.000 0.000 0.104 0.000 0.896
#> TCGA-06-0162-01A-01 4 0.2494 0.6523 0.000 0.000 0.000 0.864 0.016 0.120
#> TCGA-06-0167-01A-01 6 0.1957 0.6899 0.000 0.000 0.000 0.112 0.000 0.888
#> TCGA-06-0171-01A-02 4 0.2218 0.6634 0.000 0.000 0.000 0.884 0.012 0.104
#> TCGA-06-0173-01A-01 4 0.2628 0.6791 0.000 0.000 0.024 0.884 0.024 0.068
#> TCGA-06-0179-01A-02 6 0.2454 0.6693 0.000 0.000 0.000 0.160 0.000 0.840
#> TCGA-06-0182-01A-01 4 0.3900 0.6398 0.004 0.000 0.128 0.796 0.052 0.020
#> TCGA-06-0185-01A-01 4 0.3938 0.5076 0.000 0.000 0.312 0.672 0.012 0.004
#> TCGA-06-0195-01B-01 6 0.3464 0.4620 0.000 0.000 0.000 0.312 0.000 0.688
#> TCGA-06-0208-01B-01 4 0.3558 0.6292 0.000 0.000 0.160 0.792 0.004 0.044
#> TCGA-06-0214-01A-02 4 0.2786 0.6475 0.000 0.000 0.000 0.860 0.084 0.056
#> TCGA-06-0219-01A-01 4 0.3756 0.4848 0.000 0.000 0.000 0.712 0.020 0.268
#> TCGA-06-0221-01A-01 6 0.3854 0.1431 0.000 0.000 0.000 0.464 0.000 0.536
#> TCGA-06-0237-01A-02 4 0.1167 0.6851 0.000 0.000 0.012 0.960 0.020 0.008
#> TCGA-06-0240-01A-02 6 0.2178 0.6839 0.000 0.000 0.000 0.132 0.000 0.868
#> TCGA-08-0349-01A-01 4 0.3399 0.6693 0.000 0.000 0.016 0.832 0.064 0.088
#> TCGA-08-0380-01A-01 4 0.2934 0.6358 0.000 0.000 0.000 0.844 0.112 0.044
#> TCGA-08-0386-01A-01 3 0.6445 0.1701 0.000 0.000 0.500 0.296 0.060 0.144
#> TCGA-08-0520-01A-01 4 0.4288 0.6464 0.000 0.000 0.020 0.756 0.076 0.148
#> TCGA-02-0007-01A-01 3 0.5956 0.5154 0.012 0.000 0.612 0.208 0.132 0.036
#> TCGA-02-0009-01A-01 3 0.0260 0.9072 0.000 0.000 0.992 0.008 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.0520 0.9092 0.000 0.000 0.984 0.008 0.000 0.008
#> TCGA-02-0021-01A-01 3 0.0547 0.9063 0.000 0.000 0.980 0.020 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.2249 0.8757 0.000 0.000 0.900 0.004 0.064 0.032
#> TCGA-02-0027-01A-01 3 0.3149 0.8226 0.008 0.052 0.860 0.000 0.016 0.064
#> TCGA-02-0038-01A-01 4 0.3998 0.0443 0.000 0.000 0.492 0.504 0.004 0.000
#> TCGA-02-0043-01A-01 3 0.0551 0.9085 0.004 0.004 0.984 0.008 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.1714 0.8581 0.000 0.000 0.908 0.000 0.092 0.000
#> TCGA-02-0102-01A-01 3 0.0603 0.9063 0.000 0.000 0.980 0.004 0.016 0.000
#> TCGA-02-0260-01A-03 3 0.0891 0.9047 0.000 0.000 0.968 0.000 0.024 0.008
#> TCGA-02-0269-01B-01 3 0.0935 0.9043 0.000 0.000 0.964 0.000 0.032 0.004
#> TCGA-02-0285-01A-01 3 0.0520 0.9082 0.000 0.000 0.984 0.008 0.008 0.000
#> TCGA-02-0289-01A-01 3 0.1036 0.9066 0.000 0.000 0.964 0.008 0.024 0.004
#> TCGA-02-0290-01A-01 3 0.1647 0.9033 0.000 0.004 0.940 0.016 0.032 0.008
#> TCGA-02-0317-01A-01 3 0.1434 0.8959 0.000 0.000 0.940 0.000 0.048 0.012
#> TCGA-02-0333-01A-02 3 0.1297 0.8993 0.000 0.000 0.948 0.000 0.040 0.012
#> TCGA-02-0422-01A-01 3 0.0291 0.9080 0.000 0.000 0.992 0.004 0.004 0.000
#> TCGA-02-0430-01A-01 3 0.0632 0.9056 0.000 0.000 0.976 0.024 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0405 0.9054 0.000 0.000 0.988 0.000 0.008 0.004
#> TCGA-06-0126-01A-01 3 0.0551 0.9080 0.000 0.000 0.984 0.004 0.008 0.004
#> TCGA-06-0137-01A-03 3 0.0405 0.9060 0.000 0.000 0.988 0.000 0.008 0.004
#> TCGA-06-0145-01A-04 3 0.1387 0.8900 0.000 0.000 0.932 0.068 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.1082 0.8947 0.000 0.000 0.956 0.000 0.040 0.004
#> TCGA-06-0187-01A-01 3 0.1644 0.8817 0.000 0.000 0.920 0.076 0.004 0.000
#> TCGA-06-0211-01B-01 3 0.1858 0.8732 0.000 0.000 0.904 0.092 0.004 0.000
#> TCGA-06-0402-01A-01 3 0.1912 0.8933 0.004 0.008 0.928 0.044 0.012 0.004
#> TCGA-08-0246-01A-01 3 0.1367 0.9004 0.000 0.000 0.944 0.044 0.012 0.000
#> TCGA-08-0354-01A-01 3 0.5860 0.1424 0.000 0.008 0.508 0.380 0.072 0.032
#> TCGA-08-0355-01A-01 3 0.4300 0.7235 0.000 0.000 0.748 0.152 0.088 0.012
#> TCGA-08-0357-01A-01 3 0.0508 0.9080 0.000 0.000 0.984 0.012 0.004 0.000
#> TCGA-08-0358-01A-01 3 0.3078 0.8539 0.000 0.000 0.860 0.048 0.064 0.028
#> TCGA-08-0375-01A-01 3 0.0909 0.9074 0.000 0.000 0.968 0.020 0.012 0.000
#> TCGA-08-0511-01A-01 3 0.0146 0.9060 0.000 0.000 0.996 0.000 0.004 0.000
#> TCGA-08-0514-01A-01 3 0.0436 0.9074 0.000 0.000 0.988 0.004 0.004 0.004
#> TCGA-08-0518-01A-01 3 0.0146 0.9060 0.000 0.000 0.996 0.000 0.004 0.000
#> TCGA-08-0529-01A-02 3 0.1007 0.9016 0.000 0.000 0.956 0.044 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.0547 0.9082 0.000 0.000 0.980 0.020 0.000 0.000
#> TCGA-02-0057-01A-01 5 0.6260 0.3746 0.000 0.100 0.032 0.216 0.604 0.048
#> TCGA-02-0004-01A-01 2 0.0363 0.8440 0.000 0.988 0.000 0.000 0.012 0.000
#> TCGA-02-0006-01B-01 2 0.5035 0.6360 0.000 0.600 0.000 0.104 0.296 0.000
#> TCGA-02-0025-01A-01 2 0.0632 0.8483 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-02-0033-01A-01 2 0.0146 0.8455 0.000 0.996 0.000 0.000 0.004 0.000
#> TCGA-02-0034-01A-01 2 0.1075 0.8486 0.000 0.952 0.000 0.000 0.048 0.000
#> TCGA-02-0039-01A-01 2 0.3648 0.7738 0.000 0.740 0.000 0.004 0.240 0.016
#> TCGA-02-0051-01A-01 2 0.1820 0.8210 0.000 0.928 0.000 0.012 0.044 0.016
#> TCGA-02-0054-01A-01 4 0.4131 0.5224 0.000 0.184 0.008 0.752 0.052 0.004
#> TCGA-02-0055-01A-01 2 0.0363 0.8440 0.000 0.988 0.000 0.000 0.012 0.000
#> TCGA-02-0059-01A-01 2 0.0622 0.8428 0.000 0.980 0.000 0.000 0.012 0.008
#> TCGA-02-0064-01A-01 2 0.3468 0.7469 0.000 0.712 0.000 0.004 0.284 0.000
#> TCGA-02-0075-01A-01 2 0.1410 0.8499 0.000 0.944 0.008 0.000 0.044 0.004
#> TCGA-02-0079-01A-03 2 0.4356 0.6304 0.000 0.600 0.000 0.012 0.376 0.012
#> TCGA-02-0085-01A-01 6 0.4433 0.3028 0.000 0.304 0.000 0.016 0.024 0.656
#> TCGA-02-0086-01A-01 2 0.1592 0.8466 0.000 0.944 0.012 0.016 0.024 0.004
#> TCGA-02-0099-01A-01 2 0.2051 0.8424 0.000 0.896 0.000 0.004 0.096 0.004
#> TCGA-02-0106-01A-01 2 0.1649 0.8256 0.000 0.936 0.000 0.008 0.040 0.016
#> TCGA-02-0107-01A-01 2 0.3483 0.7672 0.000 0.748 0.000 0.016 0.236 0.000
#> TCGA-02-0111-01A-01 2 0.2340 0.8245 0.000 0.852 0.000 0.000 0.148 0.000
#> TCGA-02-0326-01A-01 6 0.4566 0.4118 0.020 0.020 0.020 0.000 0.232 0.708
#> TCGA-02-0337-01A-01 2 0.4387 0.6474 0.016 0.628 0.000 0.008 0.344 0.004
#> TCGA-06-0122-01A-01 2 0.6239 0.3627 0.000 0.444 0.216 0.008 0.328 0.004
#> TCGA-06-0124-01A-01 2 0.3186 0.8189 0.000 0.836 0.060 0.000 0.100 0.004
#> TCGA-06-0130-01A-01 2 0.0547 0.8472 0.000 0.980 0.000 0.000 0.020 0.000
#> TCGA-06-0139-01A-01 2 0.2278 0.8306 0.000 0.868 0.000 0.004 0.128 0.000
#> TCGA-06-0143-01A-01 2 0.4224 0.4744 0.000 0.512 0.008 0.000 0.476 0.004
#> TCGA-06-0147-01A-01 2 0.2838 0.8031 0.000 0.808 0.000 0.004 0.188 0.000
#> TCGA-06-0149-01A-05 4 0.6246 0.3335 0.000 0.056 0.064 0.548 0.308 0.024
#> TCGA-06-0152-01A-02 4 0.6122 0.3894 0.000 0.000 0.324 0.492 0.160 0.024
#> TCGA-06-0154-01A-02 2 0.2034 0.8418 0.000 0.912 0.024 0.000 0.060 0.004
#> TCGA-06-0164-01A-01 2 0.1082 0.8492 0.000 0.956 0.000 0.000 0.040 0.004
#> TCGA-06-0175-01A-01 2 0.4738 0.7116 0.000 0.712 0.132 0.008 0.144 0.004
#> TCGA-06-0176-01A-03 2 0.0508 0.8435 0.000 0.984 0.000 0.000 0.012 0.004
#> TCGA-06-0184-01A-01 4 0.5324 0.3697 0.000 0.104 0.004 0.636 0.240 0.016
#> TCGA-06-0189-01A-05 2 0.0260 0.8449 0.000 0.992 0.000 0.000 0.008 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.8463 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0777 0.8489 0.000 0.972 0.000 0.000 0.024 0.004
#> TCGA-06-0197-01A-02 2 0.0692 0.8493 0.000 0.976 0.000 0.000 0.020 0.004
#> TCGA-06-0210-01A-01 2 0.2846 0.8310 0.000 0.856 0.016 0.008 0.116 0.004
#> TCGA-06-0397-01A-01 2 0.0837 0.8417 0.000 0.972 0.004 0.000 0.020 0.004
#> TCGA-06-0409-01A-02 2 0.3821 0.7664 0.000 0.740 0.000 0.040 0.220 0.000
#> TCGA-06-0412-01A-01 3 0.4618 0.5925 0.000 0.032 0.684 0.252 0.032 0.000
#> TCGA-06-0644-01A-02 2 0.0909 0.8396 0.000 0.968 0.000 0.000 0.020 0.012
#> TCGA-06-0645-01A-01 2 0.4887 0.6351 0.000 0.596 0.000 0.080 0.324 0.000
#> TCGA-08-0346-01A-01 2 0.1610 0.8431 0.000 0.916 0.000 0.000 0.084 0.000
#> TCGA-08-0352-01A-01 2 0.5040 0.6770 0.000 0.664 0.156 0.000 0.172 0.008
#> TCGA-08-0360-01A-01 2 0.3742 0.6862 0.000 0.648 0.000 0.004 0.348 0.000
#> TCGA-08-0390-01A-01 2 0.3834 0.6834 0.000 0.776 0.000 0.116 0.000 0.108
#> TCGA-08-0392-01A-01 2 0.2594 0.7936 0.000 0.884 0.000 0.016 0.072 0.028
#> TCGA-08-0509-01A-01 2 0.5058 0.6311 0.000 0.600 0.000 0.108 0.292 0.000
#> TCGA-08-0510-01A-01 3 0.3614 0.7376 0.000 0.048 0.800 0.004 0.144 0.004
#> TCGA-08-0512-01A-01 2 0.0146 0.8455 0.000 0.996 0.000 0.000 0.004 0.000
#> TCGA-08-0522-01A-01 2 0.0508 0.8433 0.000 0.984 0.000 0.000 0.012 0.004
#> TCGA-12-0619-01A-01 2 0.0937 0.8491 0.000 0.960 0.000 0.000 0.040 0.000
#> TCGA-12-0620-01A-01 2 0.6041 0.5283 0.000 0.544 0.156 0.012 0.276 0.012
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> SD:NMF 167 2.11e-22 2
#> SD:NMF 152 1.54e-52 3
#> SD:NMF 169 1.15e-68 4
#> SD:NMF 132 6.25e-45 5
#> SD:NMF 145 4.24e-75 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "hclust"]
# you can also extract it by
# res = res_list["CV:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.135 0.609 0.755 0.4139 0.497 0.497
#> 3 3 0.142 0.502 0.667 0.2918 0.879 0.768
#> 4 4 0.241 0.448 0.696 0.1645 0.740 0.517
#> 5 5 0.312 0.478 0.660 0.1373 0.785 0.513
#> 6 6 0.387 0.438 0.651 0.0626 0.949 0.826
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.5178 0.7341 0.884 0.116
#> TCGA-02-0010-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.6712 0.7074 0.824 0.176
#> TCGA-02-0014-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.3431 0.7387 0.936 0.064
#> TCGA-02-0026-01B-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.5178 0.7341 0.884 0.116
#> TCGA-02-0047-01A-01 1 0.9686 0.3389 0.604 0.396
#> TCGA-02-0048-01A-01 1 0.6148 0.7243 0.848 0.152
#> TCGA-02-0060-01A-01 1 0.8661 0.5882 0.712 0.288
#> TCGA-02-0069-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.6887 0.7029 0.816 0.184
#> TCGA-02-0084-01A-03 2 0.9552 0.5222 0.376 0.624
#> TCGA-02-0087-01A-01 2 0.9552 0.5222 0.376 0.624
#> TCGA-02-0104-01A-01 2 0.2603 0.6490 0.044 0.956
#> TCGA-02-0114-01A-01 1 0.1184 0.7298 0.984 0.016
#> TCGA-02-0281-01A-01 1 0.2778 0.7341 0.952 0.048
#> TCGA-02-0321-01A-01 2 0.8207 0.7078 0.256 0.744
#> TCGA-02-0325-01A-01 1 0.0376 0.7251 0.996 0.004
#> TCGA-02-0338-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.6887 0.7029 0.816 0.184
#> TCGA-02-0439-01A-01 1 0.9775 0.2415 0.588 0.412
#> TCGA-02-0440-01A-01 1 0.5737 0.7289 0.864 0.136
#> TCGA-02-0446-01A-01 1 0.9000 0.5390 0.684 0.316
#> TCGA-06-0128-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.9248 0.4766 0.660 0.340
#> TCGA-06-0166-01A-01 1 0.9427 0.4374 0.640 0.360
#> TCGA-06-0174-01A-01 1 0.5737 0.7289 0.864 0.136
#> TCGA-06-0177-01A-01 1 0.9833 0.2865 0.576 0.424
#> TCGA-06-0238-01A-02 2 0.0000 0.6405 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.5737 0.7289 0.864 0.136
#> TCGA-06-0410-01A-01 1 0.7376 0.6802 0.792 0.208
#> TCGA-06-0413-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.5946 0.7224 0.856 0.144
#> TCGA-06-0646-01A-01 2 1.0000 0.2412 0.496 0.504
#> TCGA-06-0648-01A-01 1 0.9850 0.2731 0.572 0.428
#> TCGA-08-0245-01A-01 1 0.6247 0.7156 0.844 0.156
#> TCGA-08-0344-01A-01 1 0.8144 0.6482 0.748 0.252
#> TCGA-08-0347-01A-01 1 0.9850 0.1962 0.572 0.428
#> TCGA-08-0348-01A-01 1 0.9580 0.3885 0.620 0.380
#> TCGA-08-0350-01A-01 2 0.9635 0.4597 0.388 0.612
#> TCGA-08-0353-01A-01 1 0.6712 0.7148 0.824 0.176
#> TCGA-08-0359-01A-01 1 0.9635 0.3503 0.612 0.388
#> TCGA-08-0385-01A-01 2 0.9686 0.4446 0.396 0.604
#> TCGA-08-0517-01A-01 1 0.1633 0.7324 0.976 0.024
#> TCGA-08-0524-01A-01 1 0.4690 0.7366 0.900 0.100
#> TCGA-12-0616-01A-01 2 0.9686 0.4365 0.396 0.604
#> TCGA-12-0618-01A-01 1 0.9850 0.2731 0.572 0.428
#> TCGA-02-0089-01A-01 2 0.9833 0.3818 0.424 0.576
#> TCGA-02-0113-01A-01 1 0.9815 0.1715 0.580 0.420
#> TCGA-02-0115-01A-01 2 0.9522 0.5108 0.372 0.628
#> TCGA-02-0451-01A-01 1 0.9815 0.2451 0.580 0.420
#> TCGA-06-0132-01A-02 2 0.0000 0.6405 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.4815 0.6877 0.104 0.896
#> TCGA-06-0138-01A-02 2 0.8909 0.6665 0.308 0.692
#> TCGA-06-0160-01A-01 2 0.0000 0.6405 0.000 1.000
#> TCGA-06-0162-01A-01 2 0.0000 0.6405 0.000 1.000
#> TCGA-06-0167-01A-01 2 0.0000 0.6405 0.000 1.000
#> TCGA-06-0171-01A-02 1 0.9427 0.4374 0.640 0.360
#> TCGA-06-0173-01A-01 1 0.9044 0.5200 0.680 0.320
#> TCGA-06-0179-01A-02 2 0.0000 0.6405 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.8813 0.6758 0.300 0.700
#> TCGA-06-0185-01A-01 2 0.9775 0.5099 0.412 0.588
#> TCGA-06-0195-01B-01 2 0.0000 0.6405 0.000 1.000
#> TCGA-06-0208-01B-01 2 0.8909 0.6711 0.308 0.692
#> TCGA-06-0214-01A-02 1 0.9427 0.4374 0.640 0.360
#> TCGA-06-0219-01A-01 2 0.0000 0.6405 0.000 1.000
#> TCGA-06-0221-01A-01 2 0.0000 0.6405 0.000 1.000
#> TCGA-06-0237-01A-02 2 0.9087 0.6531 0.324 0.676
#> TCGA-06-0240-01A-02 2 0.0000 0.6405 0.000 1.000
#> TCGA-08-0349-01A-01 2 0.9963 0.3239 0.464 0.536
#> TCGA-08-0380-01A-01 2 0.9996 0.2498 0.488 0.512
#> TCGA-08-0386-01A-01 1 0.9393 0.4240 0.644 0.356
#> TCGA-08-0520-01A-01 2 0.9686 0.5376 0.396 0.604
#> TCGA-02-0007-01A-01 1 0.8499 0.5994 0.724 0.276
#> TCGA-02-0009-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-02-0016-01A-01 1 0.8386 0.6221 0.732 0.268
#> TCGA-02-0021-01A-01 1 0.4022 0.7384 0.920 0.080
#> TCGA-02-0023-01B-01 2 0.9323 0.6334 0.348 0.652
#> TCGA-02-0027-01A-01 1 0.7139 0.6983 0.804 0.196
#> TCGA-02-0038-01A-01 1 0.8016 0.6475 0.756 0.244
#> TCGA-02-0043-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-02-0070-01A-01 2 0.9491 0.6240 0.368 0.632
#> TCGA-02-0102-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-02-0260-01A-03 2 0.9522 0.5319 0.372 0.628
#> TCGA-02-0269-01B-01 2 0.9522 0.5319 0.372 0.628
#> TCGA-02-0285-01A-01 1 0.7883 0.6529 0.764 0.236
#> TCGA-02-0289-01A-01 2 0.9933 0.3302 0.452 0.548
#> TCGA-02-0290-01A-01 2 0.7056 0.7025 0.192 0.808
#> TCGA-02-0317-01A-01 2 0.9522 0.5319 0.372 0.628
#> TCGA-02-0333-01A-02 2 0.9522 0.5319 0.372 0.628
#> TCGA-02-0422-01A-01 2 0.9552 0.5734 0.376 0.624
#> TCGA-02-0430-01A-01 1 0.7883 0.6529 0.764 0.236
#> TCGA-06-0125-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-06-0126-01A-01 1 0.0000 0.7229 1.000 0.000
#> TCGA-06-0137-01A-03 1 0.4298 0.7396 0.912 0.088
#> TCGA-06-0145-01A-04 1 0.0000 0.7229 1.000 0.000
#> TCGA-06-0148-01A-01 1 0.8713 0.5697 0.708 0.292
#> TCGA-06-0187-01A-01 1 0.8443 0.6086 0.728 0.272
#> TCGA-06-0211-01B-01 2 0.9775 0.5099 0.412 0.588
#> TCGA-06-0402-01A-01 1 0.3431 0.7373 0.936 0.064
#> TCGA-08-0246-01A-01 2 0.9129 0.6638 0.328 0.672
#> TCGA-08-0354-01A-01 2 0.6148 0.7062 0.152 0.848
#> TCGA-08-0355-01A-01 2 0.9954 0.3536 0.460 0.540
#> TCGA-08-0357-01A-01 1 0.9850 0.1962 0.572 0.428
#> TCGA-08-0358-01A-01 2 0.0000 0.6405 0.000 1.000
#> TCGA-08-0375-01A-01 1 0.7056 0.7028 0.808 0.192
#> TCGA-08-0511-01A-01 1 0.8955 0.5388 0.688 0.312
#> TCGA-08-0514-01A-01 1 0.8081 0.6415 0.752 0.248
#> TCGA-08-0518-01A-01 1 0.1843 0.7323 0.972 0.028
#> TCGA-08-0529-01A-02 1 0.7883 0.6529 0.764 0.236
#> TCGA-08-0531-01A-01 1 0.8608 0.5926 0.716 0.284
#> TCGA-02-0057-01A-01 1 0.8443 0.6083 0.728 0.272
#> TCGA-02-0004-01A-01 2 0.4161 0.6850 0.084 0.916
#> TCGA-02-0006-01B-01 1 0.9323 0.4399 0.652 0.348
#> TCGA-02-0025-01A-01 2 0.0000 0.6405 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.8763 0.6907 0.296 0.704
#> TCGA-02-0034-01A-01 2 0.8763 0.6907 0.296 0.704
#> TCGA-02-0039-01A-01 2 0.9286 0.6488 0.344 0.656
#> TCGA-02-0051-01A-01 2 0.0938 0.6475 0.012 0.988
#> TCGA-02-0054-01A-01 1 0.9209 0.4722 0.664 0.336
#> TCGA-02-0055-01A-01 2 0.4161 0.6850 0.084 0.916
#> TCGA-02-0059-01A-01 2 0.4022 0.6831 0.080 0.920
#> TCGA-02-0064-01A-01 1 0.0938 0.7278 0.988 0.012
#> TCGA-02-0075-01A-01 1 0.1184 0.7295 0.984 0.016
#> TCGA-02-0079-01A-03 2 0.0000 0.6405 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.9358 0.5753 0.352 0.648
#> TCGA-02-0086-01A-01 1 0.9963 -0.0338 0.536 0.464
#> TCGA-02-0099-01A-01 1 0.9248 0.4596 0.660 0.340
#> TCGA-02-0106-01A-01 2 0.8713 0.6931 0.292 0.708
#> TCGA-02-0107-01A-01 2 0.9815 0.4995 0.420 0.580
#> TCGA-02-0111-01A-01 2 0.5737 0.7018 0.136 0.864
#> TCGA-02-0326-01A-01 2 0.0000 0.6405 0.000 1.000
#> TCGA-02-0337-01A-01 2 0.8144 0.7108 0.252 0.748
#> TCGA-06-0122-01A-01 1 0.0938 0.7278 0.988 0.012
#> TCGA-06-0124-01A-01 1 0.0938 0.7278 0.988 0.012
#> TCGA-06-0130-01A-01 2 0.8713 0.6952 0.292 0.708
#> TCGA-06-0139-01A-01 2 0.8713 0.6952 0.292 0.708
#> TCGA-06-0143-01A-01 1 0.0376 0.7251 0.996 0.004
#> TCGA-06-0147-01A-01 2 0.8713 0.6952 0.292 0.708
#> TCGA-06-0149-01A-05 2 0.9866 0.4348 0.432 0.568
#> TCGA-06-0152-01A-02 2 0.7056 0.7025 0.192 0.808
#> TCGA-06-0154-01A-02 2 0.9044 0.6779 0.320 0.680
#> TCGA-06-0164-01A-01 2 0.9044 0.6763 0.320 0.680
#> TCGA-06-0175-01A-01 2 0.9909 0.4493 0.444 0.556
#> TCGA-06-0176-01A-03 2 0.8763 0.6907 0.296 0.704
#> TCGA-06-0184-01A-01 2 0.9710 0.5294 0.400 0.600
#> TCGA-06-0189-01A-05 2 0.4161 0.6850 0.084 0.916
#> TCGA-06-0190-01A-01 2 0.9044 0.6779 0.320 0.680
#> TCGA-06-0194-01A-01 2 0.7056 0.7116 0.192 0.808
#> TCGA-06-0197-01A-02 2 0.4161 0.6850 0.084 0.916
#> TCGA-06-0210-01A-01 2 0.9286 0.6554 0.344 0.656
#> TCGA-06-0397-01A-01 2 0.9248 0.6598 0.340 0.660
#> TCGA-06-0409-01A-02 2 0.9170 0.6626 0.332 0.668
#> TCGA-06-0412-01A-01 2 0.9286 0.6554 0.344 0.656
#> TCGA-06-0644-01A-02 2 0.4022 0.6833 0.080 0.920
#> TCGA-06-0645-01A-01 2 0.9000 0.6837 0.316 0.684
#> TCGA-08-0346-01A-01 2 0.7056 0.7125 0.192 0.808
#> TCGA-08-0352-01A-01 2 0.9209 0.6663 0.336 0.664
#> TCGA-08-0360-01A-01 2 0.9209 0.6598 0.336 0.664
#> TCGA-08-0390-01A-01 2 0.7299 0.7133 0.204 0.796
#> TCGA-08-0392-01A-01 2 0.0000 0.6405 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.9248 0.6546 0.340 0.660
#> TCGA-08-0510-01A-01 1 0.2603 0.7367 0.956 0.044
#> TCGA-08-0512-01A-01 2 0.9286 0.6488 0.344 0.656
#> TCGA-08-0522-01A-01 2 0.8861 0.6870 0.304 0.696
#> TCGA-12-0619-01A-01 2 0.8813 0.6880 0.300 0.700
#> TCGA-12-0620-01A-01 2 0.6148 0.7062 0.152 0.848
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.5235 0.71067 0.812 0.152 0.036
#> TCGA-02-0010-01A-01 1 0.0237 0.69490 0.996 0.004 0.000
#> TCGA-02-0011-01B-01 1 0.5940 0.67224 0.760 0.204 0.036
#> TCGA-02-0014-01A-01 1 0.0237 0.69490 0.996 0.004 0.000
#> TCGA-02-0024-01B-01 1 0.2584 0.71661 0.928 0.064 0.008
#> TCGA-02-0026-01B-01 1 0.0000 0.69149 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.69149 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.5235 0.71067 0.812 0.152 0.036
#> TCGA-02-0047-01A-01 1 0.9065 0.30418 0.492 0.364 0.144
#> TCGA-02-0048-01A-01 1 0.6109 0.69074 0.760 0.192 0.048
#> TCGA-02-0060-01A-01 1 0.7844 0.54067 0.624 0.292 0.084
#> TCGA-02-0069-01A-01 1 0.0000 0.69149 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0424 0.69654 0.992 0.008 0.000
#> TCGA-02-0080-01A-01 1 0.6034 0.66676 0.752 0.212 0.036
#> TCGA-02-0084-01A-03 2 0.8703 0.46690 0.284 0.572 0.144
#> TCGA-02-0087-01A-01 2 0.8703 0.46690 0.284 0.572 0.144
#> TCGA-02-0104-01A-01 3 0.7279 0.38366 0.036 0.376 0.588
#> TCGA-02-0114-01A-01 1 0.1832 0.71300 0.956 0.036 0.008
#> TCGA-02-0281-01A-01 1 0.1964 0.70981 0.944 0.056 0.000
#> TCGA-02-0321-01A-01 2 0.6981 0.60151 0.132 0.732 0.136
#> TCGA-02-0325-01A-01 1 0.0592 0.69981 0.988 0.012 0.000
#> TCGA-02-0338-01A-01 1 0.0237 0.69490 0.996 0.004 0.000
#> TCGA-02-0339-01A-01 1 0.0237 0.69490 0.996 0.004 0.000
#> TCGA-02-0432-01A-02 1 0.6034 0.66676 0.752 0.212 0.036
#> TCGA-02-0439-01A-01 2 0.8341 -0.12176 0.452 0.468 0.080
#> TCGA-02-0440-01A-01 1 0.5719 0.70589 0.792 0.156 0.052
#> TCGA-02-0446-01A-01 1 0.8194 0.46935 0.572 0.340 0.088
#> TCGA-06-0128-01A-01 1 0.0000 0.69149 1.000 0.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.69149 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.69149 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 1 0.8202 0.38973 0.544 0.376 0.080
#> TCGA-06-0166-01A-01 1 0.8288 0.33008 0.512 0.408 0.080
#> TCGA-06-0174-01A-01 1 0.5719 0.70589 0.792 0.156 0.052
#> TCGA-06-0177-01A-01 1 0.9405 0.31814 0.496 0.300 0.204
#> TCGA-06-0238-01A-02 2 0.6168 -0.15324 0.000 0.588 0.412
#> TCGA-06-0241-01A-02 1 0.5719 0.70589 0.792 0.156 0.052
#> TCGA-06-0410-01A-01 1 0.7148 0.65413 0.716 0.176 0.108
#> TCGA-06-0413-01A-01 1 0.0237 0.69490 0.996 0.004 0.000
#> TCGA-06-0414-01A-01 1 0.5863 0.69987 0.796 0.120 0.084
#> TCGA-06-0646-01A-01 2 0.7228 0.36631 0.364 0.600 0.036
#> TCGA-06-0648-01A-01 1 0.9423 0.30728 0.492 0.304 0.204
#> TCGA-08-0245-01A-01 1 0.6168 0.69352 0.780 0.124 0.096
#> TCGA-08-0344-01A-01 1 0.6999 0.60692 0.680 0.268 0.052
#> TCGA-08-0347-01A-01 2 0.8892 -0.10045 0.436 0.444 0.120
#> TCGA-08-0348-01A-01 1 0.8957 0.29684 0.492 0.376 0.132
#> TCGA-08-0350-01A-01 2 0.9653 0.31998 0.312 0.456 0.232
#> TCGA-08-0353-01A-01 1 0.6586 0.67375 0.728 0.216 0.056
#> TCGA-08-0359-01A-01 1 0.8619 0.25726 0.480 0.420 0.100
#> TCGA-08-0385-01A-01 2 0.9679 0.30463 0.320 0.448 0.232
#> TCGA-08-0517-01A-01 1 0.2173 0.71616 0.944 0.048 0.008
#> TCGA-08-0524-01A-01 1 0.3454 0.71260 0.888 0.104 0.008
#> TCGA-12-0616-01A-01 2 0.9654 0.29986 0.320 0.452 0.228
#> TCGA-12-0618-01A-01 1 0.9423 0.30728 0.492 0.304 0.204
#> TCGA-02-0089-01A-01 3 0.9956 -0.13484 0.328 0.296 0.376
#> TCGA-02-0113-01A-01 2 0.8370 0.04835 0.416 0.500 0.084
#> TCGA-02-0115-01A-01 3 0.9757 0.00918 0.268 0.288 0.444
#> TCGA-02-0451-01A-01 1 0.9062 0.18068 0.452 0.412 0.136
#> TCGA-06-0132-01A-02 3 0.1753 0.62941 0.000 0.048 0.952
#> TCGA-06-0133-01A-02 3 0.7559 0.34950 0.056 0.336 0.608
#> TCGA-06-0138-01A-02 2 0.8994 0.44433 0.184 0.556 0.260
#> TCGA-06-0160-01A-01 3 0.0892 0.62532 0.000 0.020 0.980
#> TCGA-06-0162-01A-01 3 0.6235 0.38454 0.000 0.436 0.564
#> TCGA-06-0167-01A-01 3 0.0892 0.62532 0.000 0.020 0.980
#> TCGA-06-0171-01A-02 1 0.8288 0.33008 0.512 0.408 0.080
#> TCGA-06-0173-01A-01 1 0.7853 0.41964 0.556 0.384 0.060
#> TCGA-06-0179-01A-02 3 0.1753 0.62941 0.000 0.048 0.952
#> TCGA-06-0182-01A-01 2 0.8683 0.47982 0.172 0.592 0.236
#> TCGA-06-0185-01A-01 2 0.8880 0.45538 0.268 0.564 0.168
#> TCGA-06-0195-01B-01 3 0.1753 0.62941 0.000 0.048 0.952
#> TCGA-06-0208-01B-01 2 0.8953 0.45486 0.180 0.560 0.260
#> TCGA-06-0214-01A-02 1 0.8288 0.33008 0.512 0.408 0.080
#> TCGA-06-0219-01A-01 3 0.6235 0.38454 0.000 0.436 0.564
#> TCGA-06-0221-01A-01 3 0.6235 0.38454 0.000 0.436 0.564
#> TCGA-06-0237-01A-02 2 0.9092 0.46984 0.200 0.548 0.252
#> TCGA-06-0240-01A-02 3 0.0892 0.62532 0.000 0.020 0.980
#> TCGA-08-0349-01A-01 2 0.8468 0.40731 0.308 0.576 0.116
#> TCGA-08-0380-01A-01 2 0.8476 0.33525 0.332 0.560 0.108
#> TCGA-08-0386-01A-01 1 0.8347 0.31685 0.512 0.404 0.084
#> TCGA-08-0520-01A-01 2 0.8388 0.54281 0.248 0.612 0.140
#> TCGA-02-0007-01A-01 1 0.7748 0.50670 0.596 0.340 0.064
#> TCGA-02-0009-01A-01 1 0.1163 0.70704 0.972 0.028 0.000
#> TCGA-02-0016-01A-01 1 0.7507 0.57477 0.644 0.288 0.068
#> TCGA-02-0021-01A-01 1 0.4326 0.71578 0.844 0.144 0.012
#> TCGA-02-0023-01B-01 2 0.7782 0.59781 0.208 0.668 0.124
#> TCGA-02-0027-01A-01 1 0.6578 0.65651 0.724 0.224 0.052
#> TCGA-02-0038-01A-01 1 0.7065 0.56608 0.644 0.316 0.040
#> TCGA-02-0043-01A-01 1 0.1163 0.70704 0.972 0.028 0.000
#> TCGA-02-0070-01A-01 2 0.5503 0.63561 0.208 0.772 0.020
#> TCGA-02-0102-01A-01 1 0.1163 0.70704 0.972 0.028 0.000
#> TCGA-02-0260-01A-03 2 0.8722 0.48265 0.272 0.576 0.152
#> TCGA-02-0269-01B-01 2 0.8722 0.48265 0.272 0.576 0.152
#> TCGA-02-0285-01A-01 1 0.6742 0.57020 0.656 0.316 0.028
#> TCGA-02-0289-01A-01 2 0.9015 0.33107 0.348 0.508 0.144
#> TCGA-02-0290-01A-01 2 0.7731 0.45586 0.108 0.664 0.228
#> TCGA-02-0317-01A-01 2 0.8722 0.48265 0.272 0.576 0.152
#> TCGA-02-0333-01A-02 2 0.8722 0.48265 0.272 0.576 0.152
#> TCGA-02-0422-01A-01 2 0.7605 0.56737 0.252 0.660 0.088
#> TCGA-02-0430-01A-01 1 0.6742 0.57020 0.656 0.316 0.028
#> TCGA-06-0125-01A-01 1 0.1163 0.70704 0.972 0.028 0.000
#> TCGA-06-0126-01A-01 1 0.1163 0.70704 0.972 0.028 0.000
#> TCGA-06-0137-01A-03 1 0.4413 0.72137 0.852 0.124 0.024
#> TCGA-06-0145-01A-04 1 0.1411 0.70955 0.964 0.036 0.000
#> TCGA-06-0148-01A-01 1 0.7140 0.51417 0.632 0.328 0.040
#> TCGA-06-0187-01A-01 1 0.7230 0.52012 0.616 0.344 0.040
#> TCGA-06-0211-01B-01 2 0.8880 0.45538 0.268 0.564 0.168
#> TCGA-06-0402-01A-01 1 0.3845 0.71915 0.872 0.116 0.012
#> TCGA-08-0246-01A-01 2 0.7133 0.61747 0.192 0.712 0.096
#> TCGA-08-0354-01A-01 2 0.5295 0.49854 0.036 0.808 0.156
#> TCGA-08-0355-01A-01 2 0.8268 0.42714 0.328 0.576 0.096
#> TCGA-08-0357-01A-01 2 0.8892 -0.10045 0.436 0.444 0.120
#> TCGA-08-0358-01A-01 2 0.6111 -0.12517 0.000 0.604 0.396
#> TCGA-08-0375-01A-01 1 0.6523 0.65964 0.724 0.228 0.048
#> TCGA-08-0511-01A-01 1 0.7885 0.49642 0.592 0.336 0.072
#> TCGA-08-0514-01A-01 1 0.6828 0.57354 0.656 0.312 0.032
#> TCGA-08-0518-01A-01 1 0.2280 0.71646 0.940 0.052 0.008
#> TCGA-08-0529-01A-02 1 0.6742 0.57020 0.656 0.316 0.028
#> TCGA-08-0531-01A-01 1 0.7328 0.51120 0.612 0.344 0.044
#> TCGA-02-0057-01A-01 1 0.7742 0.47973 0.584 0.356 0.060
#> TCGA-02-0004-01A-01 2 0.4121 0.38072 0.000 0.832 0.168
#> TCGA-02-0006-01B-01 1 0.7979 0.24129 0.500 0.440 0.060
#> TCGA-02-0025-01A-01 2 0.6079 -0.10779 0.000 0.612 0.388
#> TCGA-02-0033-01A-01 2 0.4209 0.62447 0.120 0.860 0.020
#> TCGA-02-0034-01A-01 2 0.4068 0.62520 0.120 0.864 0.016
#> TCGA-02-0039-01A-01 2 0.5292 0.64062 0.172 0.800 0.028
#> TCGA-02-0051-01A-01 2 0.5988 0.00994 0.000 0.632 0.368
#> TCGA-02-0054-01A-01 1 0.7890 0.27625 0.512 0.432 0.056
#> TCGA-02-0055-01A-01 2 0.4002 0.38207 0.000 0.840 0.160
#> TCGA-02-0059-01A-01 2 0.4178 0.37296 0.000 0.828 0.172
#> TCGA-02-0064-01A-01 1 0.2448 0.71420 0.924 0.076 0.000
#> TCGA-02-0075-01A-01 1 0.2625 0.71556 0.916 0.084 0.000
#> TCGA-02-0079-01A-03 2 0.6079 -0.10779 0.000 0.612 0.388
#> TCGA-02-0085-01A-01 3 0.9730 -0.04998 0.228 0.352 0.420
#> TCGA-02-0086-01A-01 2 0.8362 0.20857 0.384 0.528 0.088
#> TCGA-02-0099-01A-01 1 0.8107 0.28441 0.508 0.424 0.068
#> TCGA-02-0106-01A-01 2 0.3995 0.62478 0.116 0.868 0.016
#> TCGA-02-0107-01A-01 2 0.7053 0.56751 0.244 0.692 0.064
#> TCGA-02-0111-01A-01 2 0.4418 0.46962 0.020 0.848 0.132
#> TCGA-02-0326-01A-01 2 0.6095 -0.11870 0.000 0.608 0.392
#> TCGA-02-0337-01A-01 2 0.4399 0.61524 0.092 0.864 0.044
#> TCGA-06-0122-01A-01 1 0.2448 0.71420 0.924 0.076 0.000
#> TCGA-06-0124-01A-01 1 0.2448 0.71420 0.924 0.076 0.000
#> TCGA-06-0130-01A-01 2 0.3987 0.61830 0.108 0.872 0.020
#> TCGA-06-0139-01A-01 2 0.3987 0.61830 0.108 0.872 0.020
#> TCGA-06-0143-01A-01 1 0.1289 0.70897 0.968 0.032 0.000
#> TCGA-06-0147-01A-01 2 0.3987 0.61830 0.108 0.872 0.020
#> TCGA-06-0149-01A-05 2 0.8371 0.49412 0.292 0.592 0.116
#> TCGA-06-0152-01A-02 2 0.7731 0.45586 0.108 0.664 0.228
#> TCGA-06-0154-01A-02 2 0.4326 0.63633 0.144 0.844 0.012
#> TCGA-06-0164-01A-01 2 0.4748 0.63431 0.144 0.832 0.024
#> TCGA-06-0175-01A-01 2 0.6387 0.50565 0.300 0.680 0.020
#> TCGA-06-0176-01A-03 2 0.4068 0.62520 0.120 0.864 0.016
#> TCGA-06-0184-01A-01 2 0.8311 0.52268 0.252 0.616 0.132
#> TCGA-06-0189-01A-05 2 0.4121 0.38072 0.000 0.832 0.168
#> TCGA-06-0190-01A-01 2 0.4326 0.63633 0.144 0.844 0.012
#> TCGA-06-0194-01A-01 2 0.5897 0.55034 0.076 0.792 0.132
#> TCGA-06-0197-01A-02 2 0.4121 0.38072 0.000 0.832 0.168
#> TCGA-06-0210-01A-01 2 0.4749 0.63515 0.172 0.816 0.012
#> TCGA-06-0397-01A-01 2 0.4634 0.63131 0.164 0.824 0.012
#> TCGA-06-0409-01A-02 2 0.4602 0.63873 0.152 0.832 0.016
#> TCGA-06-0412-01A-01 2 0.4749 0.63515 0.172 0.816 0.012
#> TCGA-06-0644-01A-02 2 0.4178 0.37388 0.000 0.828 0.172
#> TCGA-06-0645-01A-01 2 0.5558 0.63769 0.152 0.800 0.048
#> TCGA-08-0346-01A-01 2 0.5667 0.55159 0.060 0.800 0.140
#> TCGA-08-0352-01A-01 2 0.6229 0.62751 0.172 0.764 0.064
#> TCGA-08-0360-01A-01 2 0.4575 0.63898 0.160 0.828 0.012
#> TCGA-08-0390-01A-01 2 0.6625 0.55207 0.080 0.744 0.176
#> TCGA-08-0392-01A-01 2 0.6045 -0.03002 0.000 0.620 0.380
#> TCGA-08-0509-01A-01 2 0.5298 0.63774 0.164 0.804 0.032
#> TCGA-08-0510-01A-01 1 0.3500 0.71971 0.880 0.116 0.004
#> TCGA-08-0512-01A-01 2 0.5292 0.64062 0.172 0.800 0.028
#> TCGA-08-0522-01A-01 2 0.4349 0.62741 0.128 0.852 0.020
#> TCGA-12-0619-01A-01 2 0.4139 0.62737 0.124 0.860 0.016
#> TCGA-12-0620-01A-01 2 0.5295 0.49854 0.036 0.808 0.156
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.5101 0.6874 0.756 0.196 0.032 0.016
#> TCGA-02-0010-01A-01 1 0.0707 0.7284 0.980 0.000 0.020 0.000
#> TCGA-02-0011-01B-01 1 0.6222 0.5189 0.628 0.312 0.040 0.020
#> TCGA-02-0014-01A-01 1 0.0707 0.7284 0.980 0.000 0.020 0.000
#> TCGA-02-0024-01B-01 1 0.3790 0.7331 0.840 0.132 0.024 0.004
#> TCGA-02-0026-01B-01 1 0.1913 0.7447 0.940 0.040 0.020 0.000
#> TCGA-02-0028-01A-01 1 0.0592 0.7283 0.984 0.000 0.016 0.000
#> TCGA-02-0046-01A-01 1 0.5101 0.6874 0.756 0.196 0.032 0.016
#> TCGA-02-0047-01A-01 2 0.7743 0.3127 0.304 0.540 0.040 0.116
#> TCGA-02-0048-01A-01 1 0.5932 0.5771 0.660 0.288 0.028 0.024
#> TCGA-02-0060-01A-01 1 0.7369 0.1221 0.460 0.436 0.068 0.036
#> TCGA-02-0069-01A-01 1 0.0592 0.7283 0.984 0.000 0.016 0.000
#> TCGA-02-0074-01A-01 1 0.0895 0.7400 0.976 0.020 0.004 0.000
#> TCGA-02-0080-01A-01 1 0.6300 0.5095 0.624 0.312 0.044 0.020
#> TCGA-02-0084-01A-03 2 0.7442 0.2110 0.176 0.456 0.368 0.000
#> TCGA-02-0087-01A-01 2 0.7442 0.2110 0.176 0.456 0.368 0.000
#> TCGA-02-0104-01A-01 3 0.5275 0.3994 0.016 0.088 0.776 0.120
#> TCGA-02-0114-01A-01 1 0.2466 0.7473 0.916 0.056 0.028 0.000
#> TCGA-02-0281-01A-01 1 0.3051 0.7405 0.884 0.088 0.028 0.000
#> TCGA-02-0321-01A-01 2 0.5681 0.3898 0.036 0.704 0.240 0.020
#> TCGA-02-0325-01A-01 1 0.1890 0.7528 0.936 0.056 0.008 0.000
#> TCGA-02-0338-01A-01 1 0.0707 0.7284 0.980 0.000 0.020 0.000
#> TCGA-02-0339-01A-01 1 0.1042 0.7326 0.972 0.008 0.020 0.000
#> TCGA-02-0432-01A-02 1 0.6300 0.5095 0.624 0.312 0.044 0.020
#> TCGA-02-0439-01A-01 2 0.6690 0.4313 0.264 0.640 0.056 0.040
#> TCGA-02-0440-01A-01 1 0.5505 0.6758 0.736 0.200 0.044 0.020
#> TCGA-02-0446-01A-01 2 0.6943 0.1487 0.400 0.520 0.032 0.048
#> TCGA-06-0128-01A-01 1 0.0188 0.7308 0.996 0.000 0.004 0.000
#> TCGA-06-0129-01A-01 1 0.0188 0.7308 0.996 0.000 0.004 0.000
#> TCGA-06-0146-01A-01 1 0.1913 0.7447 0.940 0.040 0.020 0.000
#> TCGA-06-0156-01A-01 2 0.6707 0.2621 0.364 0.564 0.032 0.040
#> TCGA-06-0166-01A-01 2 0.7030 0.2975 0.348 0.560 0.052 0.040
#> TCGA-06-0174-01A-01 1 0.5505 0.6758 0.736 0.200 0.044 0.020
#> TCGA-06-0177-01A-01 2 0.8816 0.0797 0.352 0.376 0.220 0.052
#> TCGA-06-0238-01A-02 3 0.4406 0.6263 0.000 0.192 0.780 0.028
#> TCGA-06-0241-01A-02 1 0.5505 0.6758 0.736 0.200 0.044 0.020
#> TCGA-06-0410-01A-01 1 0.7216 0.5635 0.624 0.236 0.092 0.048
#> TCGA-06-0413-01A-01 1 0.1042 0.7326 0.972 0.008 0.020 0.000
#> TCGA-06-0414-01A-01 1 0.5936 0.6803 0.728 0.176 0.064 0.032
#> TCGA-06-0646-01A-01 2 0.5943 0.5686 0.216 0.696 0.080 0.008
#> TCGA-06-0648-01A-01 2 0.8814 0.0945 0.348 0.380 0.220 0.052
#> TCGA-08-0245-01A-01 1 0.6415 0.6535 0.696 0.192 0.068 0.044
#> TCGA-08-0344-01A-01 1 0.7233 0.3080 0.528 0.364 0.084 0.024
#> TCGA-08-0347-01A-01 2 0.7419 0.4298 0.260 0.600 0.076 0.064
#> TCGA-08-0348-01A-01 2 0.7997 0.2623 0.328 0.508 0.112 0.052
#> TCGA-08-0350-01A-01 2 0.8776 0.2901 0.204 0.412 0.328 0.056
#> TCGA-08-0353-01A-01 1 0.6504 0.5403 0.620 0.304 0.052 0.024
#> TCGA-08-0359-01A-01 2 0.7002 0.3587 0.308 0.592 0.040 0.060
#> TCGA-08-0385-01A-01 2 0.8762 0.3011 0.204 0.420 0.320 0.056
#> TCGA-08-0517-01A-01 1 0.2915 0.7474 0.892 0.080 0.028 0.000
#> TCGA-08-0524-01A-01 1 0.4640 0.6896 0.776 0.188 0.032 0.004
#> TCGA-12-0616-01A-01 2 0.8815 0.2893 0.212 0.404 0.328 0.056
#> TCGA-12-0618-01A-01 2 0.8814 0.0945 0.348 0.380 0.220 0.052
#> TCGA-02-0089-01A-01 2 0.8328 0.2427 0.200 0.416 0.028 0.356
#> TCGA-02-0113-01A-01 2 0.6525 0.4871 0.240 0.664 0.056 0.040
#> TCGA-02-0115-01A-01 4 0.8132 -0.1777 0.152 0.392 0.032 0.424
#> TCGA-02-0451-01A-01 2 0.7518 0.3832 0.276 0.576 0.040 0.108
#> TCGA-06-0132-01A-02 4 0.1398 0.7626 0.000 0.040 0.004 0.956
#> TCGA-06-0133-01A-02 4 0.7291 0.1757 0.004 0.292 0.164 0.540
#> TCGA-06-0138-01A-02 2 0.8045 0.3449 0.084 0.528 0.304 0.084
#> TCGA-06-0160-01A-01 4 0.0469 0.7605 0.000 0.012 0.000 0.988
#> TCGA-06-0162-01A-01 3 0.6375 0.3648 0.000 0.104 0.624 0.272
#> TCGA-06-0167-01A-01 4 0.0469 0.7605 0.000 0.012 0.000 0.988
#> TCGA-06-0171-01A-02 2 0.7030 0.2975 0.348 0.560 0.052 0.040
#> TCGA-06-0173-01A-01 2 0.6533 0.1905 0.388 0.552 0.032 0.028
#> TCGA-06-0179-01A-02 4 0.1398 0.7626 0.000 0.040 0.004 0.956
#> TCGA-06-0182-01A-01 2 0.7982 0.3241 0.084 0.524 0.316 0.076
#> TCGA-06-0185-01A-01 2 0.8063 0.4977 0.156 0.584 0.176 0.084
#> TCGA-06-0195-01B-01 4 0.1398 0.7626 0.000 0.040 0.004 0.956
#> TCGA-06-0208-01B-01 2 0.8213 0.3756 0.088 0.540 0.264 0.108
#> TCGA-06-0214-01A-02 2 0.7030 0.2975 0.348 0.560 0.052 0.040
#> TCGA-06-0219-01A-01 3 0.6375 0.3648 0.000 0.104 0.624 0.272
#> TCGA-06-0221-01A-01 3 0.6375 0.3648 0.000 0.104 0.624 0.272
#> TCGA-06-0237-01A-02 2 0.7800 0.4090 0.084 0.572 0.264 0.080
#> TCGA-06-0240-01A-02 4 0.0469 0.7605 0.000 0.012 0.000 0.988
#> TCGA-08-0349-01A-01 2 0.6373 0.5711 0.144 0.716 0.092 0.048
#> TCGA-08-0380-01A-01 2 0.6297 0.5673 0.132 0.720 0.108 0.040
#> TCGA-08-0386-01A-01 2 0.7064 0.3020 0.336 0.568 0.048 0.048
#> TCGA-08-0520-01A-01 2 0.6372 0.5344 0.088 0.704 0.172 0.036
#> TCGA-02-0007-01A-01 2 0.6957 0.1064 0.408 0.512 0.048 0.032
#> TCGA-02-0009-01A-01 1 0.1557 0.7513 0.944 0.056 0.000 0.000
#> TCGA-02-0016-01A-01 1 0.7118 0.2014 0.488 0.420 0.068 0.024
#> TCGA-02-0021-01A-01 1 0.4475 0.6661 0.748 0.240 0.008 0.004
#> TCGA-02-0023-01B-01 2 0.6058 0.4968 0.072 0.736 0.144 0.048
#> TCGA-02-0027-01A-01 1 0.6326 0.5103 0.624 0.308 0.052 0.016
#> TCGA-02-0038-01A-01 1 0.6461 0.1267 0.488 0.460 0.032 0.020
#> TCGA-02-0043-01A-01 1 0.1557 0.7513 0.944 0.056 0.000 0.000
#> TCGA-02-0070-01A-01 2 0.4362 0.5177 0.076 0.828 0.088 0.008
#> TCGA-02-0102-01A-01 1 0.1557 0.7513 0.944 0.056 0.000 0.000
#> TCGA-02-0260-01A-03 2 0.7165 0.2562 0.140 0.488 0.372 0.000
#> TCGA-02-0269-01B-01 2 0.7165 0.2562 0.140 0.488 0.372 0.000
#> TCGA-02-0285-01A-01 1 0.6093 0.1677 0.508 0.456 0.024 0.012
#> TCGA-02-0289-01A-01 2 0.7231 0.4191 0.192 0.540 0.268 0.000
#> TCGA-02-0290-01A-01 3 0.5902 0.2130 0.020 0.484 0.488 0.008
#> TCGA-02-0317-01A-01 2 0.7165 0.2562 0.140 0.488 0.372 0.000
#> TCGA-02-0333-01A-02 2 0.7165 0.2562 0.140 0.488 0.372 0.000
#> TCGA-02-0422-01A-01 2 0.7132 0.4875 0.160 0.612 0.212 0.016
#> TCGA-02-0430-01A-01 1 0.6093 0.1677 0.508 0.456 0.024 0.012
#> TCGA-06-0125-01A-01 1 0.1557 0.7513 0.944 0.056 0.000 0.000
#> TCGA-06-0126-01A-01 1 0.1557 0.7513 0.944 0.056 0.000 0.000
#> TCGA-06-0137-01A-03 1 0.4606 0.7027 0.772 0.200 0.020 0.008
#> TCGA-06-0145-01A-04 1 0.1792 0.7520 0.932 0.068 0.000 0.000
#> TCGA-06-0148-01A-01 1 0.6894 0.2748 0.512 0.376 0.112 0.000
#> TCGA-06-0187-01A-01 2 0.6459 -0.0232 0.456 0.492 0.032 0.020
#> TCGA-06-0211-01B-01 2 0.8063 0.4977 0.156 0.584 0.176 0.084
#> TCGA-06-0402-01A-01 1 0.4114 0.7004 0.788 0.200 0.008 0.004
#> TCGA-08-0246-01A-01 2 0.5522 0.4793 0.072 0.756 0.152 0.020
#> TCGA-08-0354-01A-01 2 0.5345 -0.0924 0.004 0.584 0.404 0.008
#> TCGA-08-0355-01A-01 2 0.6529 0.5300 0.176 0.680 0.124 0.020
#> TCGA-08-0357-01A-01 2 0.7419 0.4298 0.260 0.600 0.076 0.064
#> TCGA-08-0358-01A-01 3 0.3978 0.6340 0.000 0.192 0.796 0.012
#> TCGA-08-0375-01A-01 1 0.6503 0.4942 0.608 0.316 0.060 0.016
#> TCGA-08-0511-01A-01 2 0.7060 0.0460 0.428 0.488 0.036 0.048
#> TCGA-08-0514-01A-01 1 0.6099 0.1521 0.500 0.464 0.024 0.012
#> TCGA-08-0518-01A-01 1 0.3043 0.7506 0.876 0.112 0.008 0.004
#> TCGA-08-0529-01A-02 1 0.6093 0.1677 0.508 0.456 0.024 0.012
#> TCGA-08-0531-01A-01 2 0.6380 -0.0347 0.460 0.492 0.028 0.020
#> TCGA-02-0057-01A-01 2 0.6966 0.1124 0.408 0.512 0.044 0.036
#> TCGA-02-0004-01A-01 2 0.5296 -0.4504 0.000 0.496 0.496 0.008
#> TCGA-02-0006-01B-01 2 0.6619 0.3760 0.304 0.616 0.044 0.036
#> TCGA-02-0025-01A-01 3 0.4011 0.6383 0.000 0.208 0.784 0.008
#> TCGA-02-0033-01A-01 2 0.3160 0.4088 0.004 0.868 0.120 0.008
#> TCGA-02-0034-01A-01 2 0.3102 0.4117 0.004 0.872 0.116 0.008
#> TCGA-02-0039-01A-01 2 0.3402 0.4935 0.032 0.880 0.076 0.012
#> TCGA-02-0051-01A-01 3 0.4422 0.6517 0.000 0.256 0.736 0.008
#> TCGA-02-0054-01A-01 2 0.6594 0.3579 0.316 0.608 0.044 0.032
#> TCGA-02-0055-01A-01 2 0.5294 -0.4413 0.000 0.508 0.484 0.008
#> TCGA-02-0059-01A-01 3 0.5285 0.4760 0.000 0.468 0.524 0.008
#> TCGA-02-0064-01A-01 1 0.2593 0.7475 0.892 0.104 0.000 0.004
#> TCGA-02-0075-01A-01 1 0.2714 0.7460 0.884 0.112 0.000 0.004
#> TCGA-02-0079-01A-03 3 0.4011 0.6383 0.000 0.208 0.784 0.008
#> TCGA-02-0085-01A-01 2 0.7869 0.1195 0.120 0.448 0.032 0.400
#> TCGA-02-0086-01A-01 2 0.6680 0.5318 0.212 0.668 0.084 0.036
#> TCGA-02-0099-01A-01 2 0.6702 0.3604 0.308 0.608 0.052 0.032
#> TCGA-02-0106-01A-01 2 0.3326 0.3973 0.004 0.856 0.132 0.008
#> TCGA-02-0107-01A-01 2 0.5391 0.5381 0.088 0.784 0.088 0.040
#> TCGA-02-0111-01A-01 2 0.5236 -0.2821 0.000 0.560 0.432 0.008
#> TCGA-02-0326-01A-01 3 0.4059 0.6349 0.000 0.200 0.788 0.012
#> TCGA-02-0337-01A-01 2 0.4301 0.3672 0.012 0.788 0.192 0.008
#> TCGA-06-0122-01A-01 1 0.2593 0.7475 0.892 0.104 0.000 0.004
#> TCGA-06-0124-01A-01 1 0.2593 0.7475 0.892 0.104 0.000 0.004
#> TCGA-06-0130-01A-01 2 0.3401 0.3678 0.000 0.840 0.152 0.008
#> TCGA-06-0139-01A-01 2 0.3401 0.3678 0.000 0.840 0.152 0.008
#> TCGA-06-0143-01A-01 1 0.1637 0.7524 0.940 0.060 0.000 0.000
#> TCGA-06-0147-01A-01 2 0.3401 0.3678 0.000 0.840 0.152 0.008
#> TCGA-06-0149-01A-05 2 0.5931 0.5599 0.124 0.740 0.108 0.028
#> TCGA-06-0152-01A-02 3 0.5902 0.2130 0.020 0.484 0.488 0.008
#> TCGA-06-0154-01A-02 2 0.3093 0.4575 0.020 0.884 0.092 0.004
#> TCGA-06-0164-01A-01 2 0.3564 0.4365 0.016 0.860 0.112 0.012
#> TCGA-06-0175-01A-01 2 0.5648 0.5431 0.160 0.740 0.088 0.012
#> TCGA-06-0176-01A-03 2 0.3102 0.4117 0.004 0.872 0.116 0.008
#> TCGA-06-0184-01A-01 2 0.7216 0.5335 0.116 0.652 0.172 0.060
#> TCGA-06-0189-01A-05 3 0.5288 0.4686 0.000 0.472 0.520 0.008
#> TCGA-06-0190-01A-01 2 0.3093 0.4575 0.020 0.884 0.092 0.004
#> TCGA-06-0194-01A-01 2 0.4814 0.0977 0.000 0.676 0.316 0.008
#> TCGA-06-0197-01A-02 3 0.5288 0.4686 0.000 0.472 0.520 0.008
#> TCGA-06-0210-01A-01 2 0.3382 0.4785 0.040 0.876 0.080 0.004
#> TCGA-06-0397-01A-01 2 0.3877 0.4569 0.044 0.852 0.096 0.008
#> TCGA-06-0409-01A-02 2 0.2790 0.4659 0.012 0.904 0.072 0.012
#> TCGA-06-0412-01A-01 2 0.3382 0.4785 0.040 0.876 0.080 0.004
#> TCGA-06-0644-01A-02 3 0.5294 0.4304 0.000 0.484 0.508 0.008
#> TCGA-06-0645-01A-01 2 0.4347 0.4660 0.036 0.832 0.108 0.024
#> TCGA-08-0346-01A-01 2 0.5060 0.2286 0.008 0.680 0.304 0.008
#> TCGA-08-0352-01A-01 2 0.4768 0.4932 0.056 0.820 0.084 0.040
#> TCGA-08-0360-01A-01 2 0.2998 0.4752 0.024 0.892 0.080 0.004
#> TCGA-08-0390-01A-01 2 0.5840 0.2185 0.012 0.656 0.296 0.036
#> TCGA-08-0392-01A-01 3 0.4319 0.6511 0.000 0.228 0.760 0.012
#> TCGA-08-0509-01A-01 2 0.3354 0.4689 0.016 0.880 0.084 0.020
#> TCGA-08-0510-01A-01 1 0.3950 0.7212 0.804 0.184 0.008 0.004
#> TCGA-08-0512-01A-01 2 0.3402 0.4935 0.032 0.880 0.076 0.012
#> TCGA-08-0522-01A-01 2 0.3246 0.4156 0.008 0.868 0.116 0.008
#> TCGA-12-0619-01A-01 2 0.3043 0.4174 0.004 0.876 0.112 0.008
#> TCGA-12-0620-01A-01 2 0.5334 -0.0791 0.004 0.588 0.400 0.008
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.4984 0.5565 0.620 0.028 0.344 0.000 0.008
#> TCGA-02-0010-01A-01 1 0.0404 0.7149 0.988 0.012 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.5377 0.2036 0.532 0.020 0.428 0.004 0.016
#> TCGA-02-0014-01A-01 1 0.0404 0.7149 0.988 0.012 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.3606 0.6702 0.816 0.024 0.152 0.000 0.008
#> TCGA-02-0026-01B-01 1 0.1717 0.7235 0.936 0.008 0.052 0.000 0.004
#> TCGA-02-0028-01A-01 1 0.0162 0.7154 0.996 0.004 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.4984 0.5565 0.620 0.028 0.344 0.000 0.008
#> TCGA-02-0047-01A-01 3 0.5763 0.5626 0.140 0.064 0.712 0.076 0.008
#> TCGA-02-0048-01A-01 1 0.5065 0.3627 0.524 0.020 0.448 0.000 0.008
#> TCGA-02-0060-01A-01 3 0.6360 0.3243 0.316 0.036 0.580 0.020 0.048
#> TCGA-02-0069-01A-01 1 0.0000 0.7157 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.1608 0.7362 0.928 0.000 0.072 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.5540 0.1785 0.524 0.024 0.428 0.004 0.020
#> TCGA-02-0084-01A-03 3 0.7351 0.2013 0.044 0.212 0.492 0.004 0.248
#> TCGA-02-0087-01A-01 3 0.7351 0.2013 0.044 0.212 0.492 0.004 0.248
#> TCGA-02-0104-01A-01 5 0.2745 0.4707 0.000 0.028 0.052 0.024 0.896
#> TCGA-02-0114-01A-01 1 0.2800 0.7207 0.888 0.024 0.072 0.000 0.016
#> TCGA-02-0281-01A-01 1 0.2866 0.7038 0.872 0.024 0.100 0.000 0.004
#> TCGA-02-0321-01A-01 3 0.6342 -0.2253 0.000 0.372 0.464 0.000 0.164
#> TCGA-02-0325-01A-01 1 0.2843 0.7382 0.848 0.008 0.144 0.000 0.000
#> TCGA-02-0338-01A-01 1 0.0404 0.7149 0.988 0.012 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0968 0.7207 0.972 0.012 0.012 0.000 0.004
#> TCGA-02-0432-01A-02 1 0.5540 0.1785 0.524 0.024 0.428 0.004 0.020
#> TCGA-02-0439-01A-01 3 0.3753 0.5733 0.076 0.080 0.832 0.000 0.012
#> TCGA-02-0440-01A-01 1 0.5351 0.5379 0.604 0.028 0.344 0.000 0.024
#> TCGA-02-0446-01A-01 3 0.4773 0.4947 0.216 0.024 0.732 0.012 0.016
#> TCGA-06-0128-01A-01 1 0.1197 0.7295 0.952 0.000 0.048 0.000 0.000
#> TCGA-06-0129-01A-01 1 0.1197 0.7295 0.952 0.000 0.048 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.1717 0.7235 0.936 0.008 0.052 0.000 0.004
#> TCGA-06-0156-01A-01 3 0.5055 0.5457 0.184 0.068 0.728 0.004 0.016
#> TCGA-06-0166-01A-01 3 0.4826 0.5531 0.172 0.044 0.752 0.004 0.028
#> TCGA-06-0174-01A-01 1 0.5351 0.5379 0.604 0.028 0.344 0.000 0.024
#> TCGA-06-0177-01A-01 3 0.7670 0.3476 0.244 0.044 0.460 0.012 0.240
#> TCGA-06-0238-01A-02 5 0.4824 0.6355 0.000 0.268 0.028 0.016 0.688
#> TCGA-06-0241-01A-02 1 0.5351 0.5379 0.604 0.028 0.344 0.000 0.024
#> TCGA-06-0410-01A-01 1 0.6571 0.4528 0.592 0.028 0.256 0.012 0.112
#> TCGA-06-0413-01A-01 1 0.1074 0.7205 0.968 0.012 0.016 0.000 0.004
#> TCGA-06-0414-01A-01 1 0.5506 0.6061 0.696 0.020 0.208 0.012 0.064
#> TCGA-06-0646-01A-01 3 0.6576 0.1567 0.116 0.376 0.484 0.000 0.024
#> TCGA-06-0648-01A-01 3 0.7654 0.3564 0.240 0.044 0.464 0.012 0.240
#> TCGA-08-0245-01A-01 1 0.5843 0.5689 0.664 0.020 0.224 0.012 0.080
#> TCGA-08-0344-01A-01 3 0.6332 0.1151 0.412 0.036 0.484 0.000 0.068
#> TCGA-08-0347-01A-01 3 0.5917 0.5618 0.140 0.084 0.704 0.012 0.060
#> TCGA-08-0348-01A-01 3 0.6686 0.4990 0.204 0.080 0.604 0.000 0.112
#> TCGA-08-0350-01A-01 3 0.7995 0.2841 0.136 0.100 0.412 0.012 0.340
#> TCGA-08-0353-01A-01 1 0.5785 0.2489 0.512 0.020 0.420 0.000 0.048
#> TCGA-08-0359-01A-01 3 0.4246 0.5824 0.120 0.044 0.808 0.016 0.012
#> TCGA-08-0385-01A-01 3 0.7917 0.3034 0.136 0.092 0.424 0.012 0.336
#> TCGA-08-0517-01A-01 1 0.3150 0.7137 0.864 0.024 0.096 0.000 0.016
#> TCGA-08-0524-01A-01 1 0.4237 0.5966 0.752 0.028 0.212 0.000 0.008
#> TCGA-12-0616-01A-01 3 0.7991 0.2802 0.140 0.096 0.408 0.012 0.344
#> TCGA-12-0618-01A-01 3 0.7654 0.3564 0.240 0.044 0.464 0.012 0.240
#> TCGA-02-0089-01A-01 3 0.6716 0.3797 0.056 0.072 0.552 0.312 0.008
#> TCGA-02-0113-01A-01 3 0.4512 0.5386 0.076 0.132 0.776 0.000 0.016
#> TCGA-02-0115-01A-01 3 0.6508 0.2193 0.028 0.076 0.504 0.384 0.008
#> TCGA-02-0451-01A-01 3 0.5256 0.5813 0.100 0.068 0.756 0.068 0.008
#> TCGA-06-0132-01A-02 4 0.1267 0.8778 0.000 0.024 0.012 0.960 0.004
#> TCGA-06-0133-01A-02 4 0.7300 0.2490 0.000 0.060 0.220 0.508 0.212
#> TCGA-06-0138-01A-02 3 0.6654 0.2839 0.000 0.136 0.508 0.024 0.332
#> TCGA-06-0160-01A-01 4 0.0162 0.8745 0.000 0.000 0.004 0.996 0.000
#> TCGA-06-0162-01A-01 5 0.5144 0.3922 0.000 0.072 0.012 0.220 0.696
#> TCGA-06-0167-01A-01 4 0.0162 0.8745 0.000 0.000 0.004 0.996 0.000
#> TCGA-06-0171-01A-02 3 0.4906 0.5532 0.172 0.044 0.748 0.004 0.032
#> TCGA-06-0173-01A-01 3 0.4709 0.5125 0.200 0.068 0.728 0.000 0.004
#> TCGA-06-0179-01A-02 4 0.1267 0.8778 0.000 0.024 0.012 0.960 0.004
#> TCGA-06-0182-01A-01 3 0.6493 0.2548 0.000 0.152 0.480 0.008 0.360
#> TCGA-06-0185-01A-01 3 0.6951 0.4268 0.040 0.128 0.596 0.024 0.212
#> TCGA-06-0195-01B-01 4 0.1267 0.8778 0.000 0.024 0.012 0.960 0.004
#> TCGA-06-0208-01B-01 3 0.6888 0.3050 0.004 0.124 0.512 0.036 0.324
#> TCGA-06-0214-01A-02 3 0.4906 0.5532 0.172 0.044 0.748 0.004 0.032
#> TCGA-06-0219-01A-01 5 0.5144 0.3922 0.000 0.072 0.012 0.220 0.696
#> TCGA-06-0221-01A-01 5 0.5144 0.3922 0.000 0.072 0.012 0.220 0.696
#> TCGA-06-0237-01A-02 3 0.6382 0.3282 0.000 0.124 0.552 0.020 0.304
#> TCGA-06-0240-01A-02 4 0.0162 0.8745 0.000 0.000 0.004 0.996 0.000
#> TCGA-08-0349-01A-01 3 0.5450 0.4062 0.016 0.204 0.704 0.020 0.056
#> TCGA-08-0380-01A-01 3 0.3944 0.4502 0.000 0.160 0.788 0.000 0.052
#> TCGA-08-0386-01A-01 3 0.3791 0.5668 0.136 0.040 0.816 0.004 0.004
#> TCGA-08-0520-01A-01 3 0.5416 0.3378 0.000 0.196 0.672 0.004 0.128
#> TCGA-02-0007-01A-01 3 0.3933 0.4943 0.196 0.020 0.776 0.000 0.008
#> TCGA-02-0009-01A-01 1 0.2773 0.7360 0.836 0.000 0.164 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.5685 0.3153 0.316 0.036 0.608 0.000 0.040
#> TCGA-02-0021-01A-01 1 0.4610 0.4947 0.596 0.016 0.388 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.6620 0.0890 0.012 0.292 0.564 0.024 0.108
#> TCGA-02-0027-01A-01 3 0.5647 -0.1577 0.468 0.028 0.476 0.000 0.028
#> TCGA-02-0038-01A-01 3 0.5152 0.3321 0.312 0.052 0.632 0.000 0.004
#> TCGA-02-0043-01A-01 1 0.2773 0.7360 0.836 0.000 0.164 0.000 0.000
#> TCGA-02-0070-01A-01 2 0.5536 0.5064 0.028 0.564 0.380 0.000 0.028
#> TCGA-02-0102-01A-01 1 0.2773 0.7360 0.836 0.000 0.164 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.7504 0.2240 0.060 0.212 0.492 0.004 0.232
#> TCGA-02-0269-01B-01 3 0.7504 0.2240 0.060 0.212 0.492 0.004 0.232
#> TCGA-02-0285-01A-01 3 0.4890 0.2983 0.332 0.040 0.628 0.000 0.000
#> TCGA-02-0289-01A-01 3 0.7493 0.3943 0.104 0.172 0.536 0.004 0.184
#> TCGA-02-0290-01A-01 5 0.6958 0.1016 0.000 0.320 0.332 0.004 0.344
#> TCGA-02-0317-01A-01 3 0.7504 0.2240 0.060 0.212 0.492 0.004 0.232
#> TCGA-02-0333-01A-02 3 0.7504 0.2240 0.060 0.212 0.492 0.004 0.232
#> TCGA-02-0422-01A-01 3 0.7106 0.1818 0.064 0.280 0.520 0.000 0.136
#> TCGA-02-0430-01A-01 3 0.4890 0.2983 0.332 0.040 0.628 0.000 0.000
#> TCGA-06-0125-01A-01 1 0.2773 0.7360 0.836 0.000 0.164 0.000 0.000
#> TCGA-06-0126-01A-01 1 0.2773 0.7360 0.836 0.000 0.164 0.000 0.000
#> TCGA-06-0137-01A-03 1 0.4264 0.5466 0.620 0.004 0.376 0.000 0.000
#> TCGA-06-0145-01A-04 1 0.3010 0.7330 0.824 0.004 0.172 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.6821 0.0978 0.400 0.092 0.456 0.000 0.052
#> TCGA-06-0187-01A-01 3 0.5171 0.4133 0.276 0.076 0.648 0.000 0.000
#> TCGA-06-0211-01B-01 3 0.6951 0.4268 0.040 0.128 0.596 0.024 0.212
#> TCGA-06-0402-01A-01 1 0.4341 0.5474 0.628 0.008 0.364 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.6557 -0.0748 0.024 0.348 0.508 0.000 0.120
#> TCGA-08-0354-01A-01 2 0.6724 0.2792 0.000 0.420 0.284 0.000 0.296
#> TCGA-08-0355-01A-01 3 0.6955 0.3282 0.100 0.256 0.556 0.000 0.088
#> TCGA-08-0357-01A-01 3 0.5917 0.5618 0.140 0.084 0.704 0.012 0.060
#> TCGA-08-0358-01A-01 5 0.4919 0.6301 0.000 0.304 0.040 0.004 0.652
#> TCGA-08-0375-01A-01 1 0.5748 0.1360 0.492 0.020 0.444 0.000 0.044
#> TCGA-08-0511-01A-01 3 0.5113 0.4429 0.252 0.024 0.692 0.020 0.012
#> TCGA-08-0514-01A-01 3 0.5145 0.3043 0.332 0.056 0.612 0.000 0.000
#> TCGA-08-0518-01A-01 1 0.3662 0.6924 0.744 0.004 0.252 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.4890 0.2983 0.332 0.040 0.628 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.5119 0.4040 0.280 0.060 0.656 0.000 0.004
#> TCGA-02-0057-01A-01 3 0.5453 0.4776 0.212 0.088 0.684 0.004 0.012
#> TCGA-02-0004-01A-01 2 0.5028 0.1149 0.000 0.564 0.036 0.000 0.400
#> TCGA-02-0006-01B-01 3 0.5078 0.5477 0.112 0.136 0.736 0.004 0.012
#> TCGA-02-0025-01A-01 5 0.5040 0.6192 0.000 0.332 0.040 0.004 0.624
#> TCGA-02-0033-01A-01 2 0.2648 0.6540 0.000 0.848 0.152 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.2773 0.6600 0.000 0.836 0.164 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.4151 0.6069 0.000 0.652 0.344 0.000 0.004
#> TCGA-02-0051-01A-01 5 0.4584 0.4441 0.000 0.312 0.028 0.000 0.660
#> TCGA-02-0054-01A-01 3 0.4931 0.5573 0.124 0.124 0.740 0.000 0.012
#> TCGA-02-0055-01A-01 2 0.5000 0.1323 0.000 0.576 0.036 0.000 0.388
#> TCGA-02-0059-01A-01 2 0.4861 0.0351 0.000 0.548 0.024 0.000 0.428
#> TCGA-02-0064-01A-01 1 0.3880 0.7208 0.784 0.028 0.184 0.000 0.004
#> TCGA-02-0075-01A-01 1 0.3997 0.7177 0.776 0.032 0.188 0.000 0.004
#> TCGA-02-0079-01A-03 5 0.5040 0.6192 0.000 0.332 0.040 0.004 0.624
#> TCGA-02-0085-01A-01 3 0.7067 0.1735 0.016 0.156 0.444 0.372 0.012
#> TCGA-02-0086-01A-01 3 0.4854 0.4866 0.072 0.196 0.724 0.000 0.008
#> TCGA-02-0099-01A-01 3 0.3722 0.5788 0.104 0.060 0.828 0.000 0.008
#> TCGA-02-0106-01A-01 2 0.3098 0.6530 0.000 0.836 0.148 0.000 0.016
#> TCGA-02-0107-01A-01 2 0.4800 0.2647 0.000 0.528 0.456 0.008 0.008
#> TCGA-02-0111-01A-01 2 0.5947 0.3090 0.000 0.556 0.132 0.000 0.312
#> TCGA-02-0326-01A-01 5 0.4991 0.6227 0.000 0.320 0.040 0.004 0.636
#> TCGA-02-0337-01A-01 2 0.5441 0.6130 0.000 0.624 0.280 0.000 0.096
#> TCGA-06-0122-01A-01 1 0.3880 0.7208 0.784 0.028 0.184 0.000 0.004
#> TCGA-06-0124-01A-01 1 0.3880 0.7208 0.784 0.028 0.184 0.000 0.004
#> TCGA-06-0130-01A-01 2 0.2052 0.5731 0.000 0.912 0.080 0.004 0.004
#> TCGA-06-0139-01A-01 2 0.2052 0.5731 0.000 0.912 0.080 0.004 0.004
#> TCGA-06-0143-01A-01 1 0.2732 0.7372 0.840 0.000 0.160 0.000 0.000
#> TCGA-06-0147-01A-01 2 0.2052 0.5731 0.000 0.912 0.080 0.004 0.004
#> TCGA-06-0149-01A-05 3 0.5474 0.2880 0.016 0.256 0.656 0.000 0.072
#> TCGA-06-0152-01A-02 5 0.6958 0.1016 0.000 0.320 0.332 0.004 0.344
#> TCGA-06-0154-01A-02 2 0.4133 0.6757 0.012 0.744 0.232 0.000 0.012
#> TCGA-06-0164-01A-01 2 0.3246 0.6684 0.008 0.808 0.184 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.5449 0.3279 0.068 0.556 0.376 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.2690 0.6557 0.000 0.844 0.156 0.000 0.000
#> TCGA-06-0184-01A-01 3 0.5863 0.3396 0.004 0.224 0.644 0.012 0.116
#> TCGA-06-0189-01A-05 2 0.4855 0.0498 0.000 0.552 0.024 0.000 0.424
#> TCGA-06-0190-01A-01 2 0.4133 0.6757 0.012 0.744 0.232 0.000 0.012
#> TCGA-06-0194-01A-01 2 0.5958 0.5195 0.000 0.592 0.204 0.000 0.204
#> TCGA-06-0197-01A-02 2 0.4855 0.0498 0.000 0.552 0.024 0.000 0.424
#> TCGA-06-0210-01A-01 2 0.4491 0.6563 0.024 0.708 0.260 0.000 0.008
#> TCGA-06-0397-01A-01 2 0.3897 0.6684 0.028 0.768 0.204 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.3684 0.6568 0.000 0.720 0.280 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.4491 0.6563 0.024 0.708 0.260 0.000 0.008
#> TCGA-06-0644-01A-02 2 0.5059 0.0907 0.000 0.548 0.036 0.000 0.416
#> TCGA-06-0645-01A-01 2 0.5965 0.5418 0.012 0.560 0.360 0.012 0.056
#> TCGA-08-0346-01A-01 2 0.6572 0.3891 0.000 0.428 0.364 0.000 0.208
#> TCGA-08-0352-01A-01 2 0.6301 0.4811 0.024 0.528 0.384 0.028 0.036
#> TCGA-08-0360-01A-01 2 0.4025 0.6522 0.000 0.700 0.292 0.000 0.008
#> TCGA-08-0390-01A-01 2 0.7112 0.3812 0.000 0.412 0.364 0.024 0.200
#> TCGA-08-0392-01A-01 5 0.4109 0.5069 0.000 0.288 0.012 0.000 0.700
#> TCGA-08-0509-01A-01 2 0.4280 0.6398 0.000 0.676 0.312 0.004 0.008
#> TCGA-08-0510-01A-01 1 0.4725 0.6538 0.680 0.036 0.280 0.000 0.004
#> TCGA-08-0512-01A-01 2 0.4151 0.6069 0.000 0.652 0.344 0.000 0.004
#> TCGA-08-0522-01A-01 2 0.2806 0.6563 0.004 0.844 0.152 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.2773 0.6606 0.000 0.836 0.164 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.6725 0.2874 0.000 0.420 0.288 0.000 0.292
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.5155 0.47135 0.556 0.004 0.060 0.000 0.008 0.372
#> TCGA-02-0010-01A-01 1 0.1364 0.66869 0.944 0.000 0.048 0.000 0.004 0.004
#> TCGA-02-0011-01B-01 1 0.5598 0.12474 0.480 0.004 0.108 0.000 0.004 0.404
#> TCGA-02-0014-01A-01 1 0.1364 0.66869 0.944 0.000 0.048 0.000 0.004 0.004
#> TCGA-02-0024-01B-01 1 0.4207 0.58194 0.752 0.004 0.064 0.000 0.008 0.172
#> TCGA-02-0026-01B-01 1 0.2209 0.67965 0.904 0.000 0.040 0.000 0.004 0.052
#> TCGA-02-0028-01A-01 1 0.1219 0.66943 0.948 0.000 0.048 0.000 0.004 0.000
#> TCGA-02-0046-01A-01 1 0.5155 0.47135 0.556 0.004 0.060 0.000 0.008 0.372
#> TCGA-02-0047-01A-01 6 0.5300 0.52244 0.100 0.064 0.016 0.076 0.012 0.732
#> TCGA-02-0048-01A-01 6 0.5255 -0.24675 0.444 0.008 0.052 0.000 0.008 0.488
#> TCGA-02-0060-01A-01 6 0.6352 0.31772 0.256 0.012 0.156 0.020 0.008 0.548
#> TCGA-02-0069-01A-01 1 0.1152 0.66997 0.952 0.000 0.044 0.000 0.004 0.000
#> TCGA-02-0074-01A-01 1 0.2928 0.69488 0.856 0.004 0.056 0.000 0.000 0.084
#> TCGA-02-0080-01A-01 1 0.5716 0.11209 0.472 0.004 0.124 0.000 0.004 0.396
#> TCGA-02-0084-01A-03 3 0.5108 0.52084 0.008 0.040 0.584 0.000 0.016 0.352
#> TCGA-02-0087-01A-01 3 0.5108 0.52084 0.008 0.040 0.584 0.000 0.016 0.352
#> TCGA-02-0104-01A-01 5 0.2618 0.48924 0.000 0.000 0.116 0.000 0.860 0.024
#> TCGA-02-0114-01A-01 1 0.3364 0.65198 0.832 0.000 0.068 0.000 0.012 0.088
#> TCGA-02-0281-01A-01 1 0.3413 0.64926 0.824 0.000 0.052 0.000 0.012 0.112
#> TCGA-02-0321-01A-01 6 0.7160 -0.03808 0.000 0.292 0.124 0.000 0.168 0.416
#> TCGA-02-0325-01A-01 1 0.3822 0.69016 0.776 0.000 0.096 0.000 0.000 0.128
#> TCGA-02-0338-01A-01 1 0.1364 0.66869 0.944 0.000 0.048 0.000 0.004 0.004
#> TCGA-02-0339-01A-01 1 0.1562 0.68082 0.940 0.000 0.032 0.000 0.004 0.024
#> TCGA-02-0432-01A-02 1 0.5716 0.11209 0.472 0.004 0.124 0.000 0.004 0.396
#> TCGA-02-0439-01A-01 6 0.3842 0.50980 0.040 0.060 0.072 0.000 0.008 0.820
#> TCGA-02-0440-01A-01 1 0.5490 0.44378 0.540 0.004 0.068 0.000 0.020 0.368
#> TCGA-02-0446-01A-01 6 0.4352 0.50997 0.164 0.016 0.036 0.012 0.008 0.764
#> TCGA-06-0128-01A-01 1 0.2384 0.69145 0.888 0.000 0.048 0.000 0.000 0.064
#> TCGA-06-0129-01A-01 1 0.2384 0.69145 0.888 0.000 0.048 0.000 0.000 0.064
#> TCGA-06-0146-01A-01 1 0.2209 0.67965 0.904 0.000 0.040 0.000 0.004 0.052
#> TCGA-06-0156-01A-01 6 0.4789 0.52735 0.136 0.076 0.032 0.004 0.008 0.744
#> TCGA-06-0166-01A-01 6 0.4643 0.52594 0.120 0.048 0.040 0.004 0.020 0.768
#> TCGA-06-0174-01A-01 1 0.5490 0.44378 0.540 0.004 0.068 0.000 0.020 0.368
#> TCGA-06-0177-01A-01 6 0.7512 0.19186 0.200 0.004 0.220 0.000 0.172 0.404
#> TCGA-06-0238-01A-02 5 0.4787 -0.01420 0.000 0.028 0.480 0.012 0.480 0.000
#> TCGA-06-0241-01A-02 1 0.5490 0.44378 0.540 0.004 0.068 0.000 0.020 0.368
#> TCGA-06-0410-01A-01 1 0.6476 0.37082 0.544 0.008 0.088 0.000 0.096 0.264
#> TCGA-06-0413-01A-01 1 0.1642 0.68059 0.936 0.000 0.032 0.000 0.004 0.028
#> TCGA-06-0414-01A-01 1 0.5424 0.52222 0.648 0.000 0.088 0.000 0.048 0.216
#> TCGA-06-0646-01A-01 6 0.6642 0.10563 0.092 0.384 0.052 0.000 0.024 0.448
#> TCGA-06-0648-01A-01 6 0.7496 0.19202 0.196 0.004 0.220 0.000 0.172 0.408
#> TCGA-08-0245-01A-01 1 0.5733 0.48442 0.616 0.000 0.088 0.000 0.064 0.232
#> TCGA-08-0344-01A-01 6 0.6622 0.14947 0.360 0.004 0.132 0.000 0.060 0.444
#> TCGA-08-0347-01A-01 6 0.6457 0.41771 0.112 0.072 0.136 0.012 0.032 0.636
#> TCGA-08-0348-01A-01 6 0.7056 0.35574 0.164 0.040 0.168 0.000 0.084 0.544
#> TCGA-08-0350-01A-01 6 0.8268 -0.04094 0.116 0.060 0.272 0.000 0.252 0.300
#> TCGA-08-0353-01A-01 1 0.6161 0.18403 0.464 0.008 0.128 0.000 0.020 0.380
#> TCGA-08-0359-01A-01 6 0.4066 0.52324 0.072 0.036 0.044 0.016 0.012 0.820
#> TCGA-08-0385-01A-01 6 0.8223 -0.02137 0.116 0.056 0.268 0.000 0.248 0.312
#> TCGA-08-0517-01A-01 1 0.3646 0.63991 0.808 0.000 0.068 0.000 0.012 0.112
#> TCGA-08-0524-01A-01 1 0.4895 0.50211 0.684 0.004 0.076 0.000 0.016 0.220
#> TCGA-12-0616-01A-01 6 0.8267 -0.03025 0.124 0.056 0.260 0.000 0.256 0.304
#> TCGA-12-0618-01A-01 6 0.7496 0.19202 0.196 0.004 0.220 0.000 0.172 0.408
#> TCGA-02-0089-01A-01 6 0.5929 0.33525 0.036 0.068 0.004 0.312 0.012 0.568
#> TCGA-02-0113-01A-01 6 0.4414 0.51306 0.052 0.092 0.036 0.000 0.032 0.788
#> TCGA-02-0115-01A-01 6 0.5785 0.20158 0.012 0.068 0.012 0.384 0.008 0.516
#> TCGA-02-0451-01A-01 6 0.4944 0.52806 0.064 0.068 0.028 0.068 0.008 0.764
#> TCGA-06-0132-01A-02 4 0.1049 0.87315 0.000 0.000 0.000 0.960 0.032 0.008
#> TCGA-06-0133-01A-02 4 0.6504 0.20915 0.000 0.020 0.016 0.504 0.240 0.220
#> TCGA-06-0138-01A-02 6 0.6170 0.22769 0.000 0.064 0.048 0.016 0.384 0.488
#> TCGA-06-0160-01A-01 4 0.0146 0.86996 0.000 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0162-01A-01 5 0.3514 0.46695 0.000 0.000 0.020 0.208 0.768 0.004
#> TCGA-06-0167-01A-01 4 0.0146 0.86996 0.000 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0171-01A-02 6 0.4656 0.52706 0.120 0.048 0.036 0.004 0.024 0.768
#> TCGA-06-0173-01A-01 6 0.4716 0.52583 0.144 0.084 0.032 0.000 0.004 0.736
#> TCGA-06-0179-01A-02 4 0.1049 0.87315 0.000 0.000 0.000 0.960 0.032 0.008
#> TCGA-06-0182-01A-01 6 0.6032 0.17126 0.000 0.092 0.044 0.000 0.408 0.456
#> TCGA-06-0185-01A-01 6 0.6475 0.37964 0.024 0.080 0.044 0.020 0.240 0.592
#> TCGA-06-0195-01B-01 4 0.1049 0.87315 0.000 0.000 0.000 0.960 0.032 0.008
#> TCGA-06-0208-01B-01 6 0.6295 0.25823 0.000 0.064 0.044 0.028 0.364 0.500
#> TCGA-06-0214-01A-02 6 0.4656 0.52706 0.120 0.048 0.036 0.004 0.024 0.768
#> TCGA-06-0219-01A-01 5 0.3514 0.46695 0.000 0.000 0.020 0.208 0.768 0.004
#> TCGA-06-0221-01A-01 5 0.3514 0.46695 0.000 0.000 0.020 0.208 0.768 0.004
#> TCGA-06-0237-01A-02 6 0.5951 0.28267 0.000 0.056 0.056 0.008 0.352 0.528
#> TCGA-06-0240-01A-02 4 0.0146 0.86996 0.000 0.000 0.000 0.996 0.000 0.004
#> TCGA-08-0349-01A-01 6 0.5777 0.42929 0.008 0.148 0.072 0.016 0.076 0.680
#> TCGA-08-0380-01A-01 6 0.4663 0.45637 0.000 0.108 0.064 0.000 0.080 0.748
#> TCGA-08-0386-01A-01 6 0.3441 0.53367 0.080 0.028 0.048 0.000 0.004 0.840
#> TCGA-08-0520-01A-01 6 0.5725 0.38779 0.000 0.128 0.072 0.000 0.156 0.644
#> TCGA-02-0007-01A-01 6 0.3783 0.50663 0.136 0.012 0.060 0.000 0.000 0.792
#> TCGA-02-0009-01A-01 1 0.4095 0.68014 0.756 0.004 0.088 0.000 0.000 0.152
#> TCGA-02-0016-01A-01 6 0.5705 0.33114 0.260 0.016 0.152 0.000 0.000 0.572
#> TCGA-02-0021-01A-01 1 0.5465 0.42165 0.508 0.016 0.080 0.000 0.000 0.396
#> TCGA-02-0023-01B-01 6 0.7293 0.26329 0.008 0.212 0.128 0.024 0.112 0.516
#> TCGA-02-0027-01A-01 6 0.5754 -0.09356 0.412 0.008 0.132 0.000 0.000 0.448
#> TCGA-02-0038-01A-01 6 0.5259 0.36290 0.252 0.072 0.028 0.000 0.004 0.644
#> TCGA-02-0043-01A-01 1 0.4143 0.67986 0.752 0.004 0.092 0.000 0.000 0.152
#> TCGA-02-0070-01A-01 2 0.5650 0.47847 0.028 0.572 0.072 0.000 0.008 0.320
#> TCGA-02-0102-01A-01 1 0.4143 0.67986 0.752 0.004 0.092 0.000 0.000 0.152
#> TCGA-02-0260-01A-03 3 0.5462 0.53756 0.044 0.032 0.560 0.000 0.008 0.356
#> TCGA-02-0269-01B-01 3 0.5462 0.53756 0.044 0.032 0.560 0.000 0.008 0.356
#> TCGA-02-0285-01A-01 6 0.4813 0.34334 0.264 0.040 0.032 0.000 0.000 0.664
#> TCGA-02-0289-01A-01 3 0.6099 0.26808 0.080 0.040 0.452 0.000 0.008 0.420
#> TCGA-02-0290-01A-01 3 0.6793 0.48204 0.000 0.104 0.496 0.000 0.156 0.244
#> TCGA-02-0317-01A-01 3 0.5462 0.53756 0.044 0.032 0.560 0.000 0.008 0.356
#> TCGA-02-0333-01A-02 3 0.5462 0.53756 0.044 0.032 0.560 0.000 0.008 0.356
#> TCGA-02-0422-01A-01 6 0.7454 0.24651 0.044 0.240 0.092 0.000 0.148 0.476
#> TCGA-02-0430-01A-01 6 0.4813 0.34334 0.264 0.040 0.032 0.000 0.000 0.664
#> TCGA-06-0125-01A-01 1 0.4095 0.68014 0.756 0.004 0.088 0.000 0.000 0.152
#> TCGA-06-0126-01A-01 1 0.4095 0.68014 0.756 0.004 0.088 0.000 0.000 0.152
#> TCGA-06-0137-01A-03 1 0.5081 0.47697 0.552 0.008 0.064 0.000 0.000 0.376
#> TCGA-06-0145-01A-04 1 0.4274 0.67621 0.744 0.008 0.088 0.000 0.000 0.160
#> TCGA-06-0148-01A-01 6 0.6706 0.00142 0.360 0.044 0.212 0.000 0.000 0.384
#> TCGA-06-0187-01A-01 6 0.5143 0.43622 0.208 0.084 0.028 0.000 0.004 0.676
#> TCGA-06-0211-01B-01 6 0.6475 0.37964 0.024 0.080 0.044 0.020 0.240 0.592
#> TCGA-06-0402-01A-01 1 0.5328 0.47776 0.536 0.008 0.088 0.000 0.000 0.368
#> TCGA-08-0246-01A-01 6 0.7293 0.11719 0.020 0.272 0.116 0.000 0.132 0.460
#> TCGA-08-0354-01A-01 5 0.7313 -0.18360 0.000 0.324 0.104 0.000 0.328 0.244
#> TCGA-08-0355-01A-01 6 0.7310 0.36272 0.076 0.164 0.120 0.000 0.100 0.540
#> TCGA-08-0357-01A-01 6 0.6457 0.41771 0.112 0.072 0.136 0.012 0.032 0.636
#> TCGA-08-0358-01A-01 3 0.4353 0.04691 0.000 0.028 0.588 0.000 0.384 0.000
#> TCGA-08-0375-01A-01 1 0.6124 0.08340 0.448 0.008 0.120 0.000 0.020 0.404
#> TCGA-08-0511-01A-01 6 0.5363 0.43890 0.200 0.032 0.060 0.020 0.004 0.684
#> TCGA-08-0514-01A-01 6 0.5314 0.31371 0.268 0.056 0.048 0.000 0.000 0.628
#> TCGA-08-0518-01A-01 1 0.4777 0.63295 0.660 0.004 0.088 0.000 0.000 0.248
#> TCGA-08-0529-01A-02 6 0.4813 0.34334 0.264 0.040 0.032 0.000 0.000 0.664
#> TCGA-08-0531-01A-01 6 0.4963 0.42671 0.216 0.060 0.032 0.000 0.004 0.688
#> TCGA-02-0057-01A-01 6 0.5376 0.49833 0.164 0.092 0.048 0.004 0.004 0.688
#> TCGA-02-0004-01A-01 2 0.4356 0.12532 0.000 0.548 0.016 0.000 0.432 0.004
#> TCGA-02-0006-01B-01 6 0.5202 0.48992 0.080 0.184 0.036 0.004 0.004 0.692
#> TCGA-02-0025-01A-01 3 0.4506 0.09113 0.000 0.044 0.608 0.000 0.348 0.000
#> TCGA-02-0033-01A-01 2 0.1663 0.65801 0.000 0.912 0.000 0.000 0.000 0.088
#> TCGA-02-0034-01A-01 2 0.1814 0.66423 0.000 0.900 0.000 0.000 0.000 0.100
#> TCGA-02-0039-01A-01 2 0.4002 0.61928 0.000 0.692 0.016 0.000 0.008 0.284
#> TCGA-02-0051-01A-01 5 0.4469 0.40822 0.000 0.276 0.052 0.000 0.668 0.004
#> TCGA-02-0054-01A-01 6 0.5004 0.49764 0.088 0.164 0.036 0.000 0.004 0.708
#> TCGA-02-0055-01A-01 2 0.4256 0.15386 0.000 0.564 0.012 0.000 0.420 0.004
#> TCGA-02-0059-01A-01 2 0.4384 0.07354 0.000 0.520 0.016 0.000 0.460 0.004
#> TCGA-02-0064-01A-01 1 0.5000 0.66049 0.704 0.032 0.088 0.000 0.004 0.172
#> TCGA-02-0075-01A-01 1 0.5099 0.65680 0.696 0.036 0.088 0.000 0.004 0.176
#> TCGA-02-0079-01A-03 3 0.4506 0.09113 0.000 0.044 0.608 0.000 0.348 0.000
#> TCGA-02-0085-01A-01 6 0.6474 0.16148 0.008 0.140 0.016 0.372 0.012 0.452
#> TCGA-02-0086-01A-01 6 0.4754 0.49710 0.048 0.152 0.024 0.000 0.032 0.744
#> TCGA-02-0099-01A-01 6 0.3847 0.51630 0.064 0.068 0.056 0.000 0.000 0.812
#> TCGA-02-0106-01A-01 2 0.2163 0.66259 0.000 0.892 0.000 0.000 0.016 0.092
#> TCGA-02-0107-01A-01 2 0.4371 0.30639 0.000 0.576 0.004 0.008 0.008 0.404
#> TCGA-02-0111-01A-01 2 0.6137 0.25844 0.000 0.508 0.052 0.000 0.336 0.104
#> TCGA-02-0326-01A-01 3 0.4319 0.10642 0.000 0.032 0.620 0.000 0.348 0.000
#> TCGA-02-0337-01A-01 2 0.5899 0.57440 0.000 0.600 0.088 0.000 0.076 0.236
#> TCGA-06-0122-01A-01 1 0.5000 0.66049 0.704 0.032 0.088 0.000 0.004 0.172
#> TCGA-06-0124-01A-01 1 0.5000 0.66049 0.704 0.032 0.088 0.000 0.004 0.172
#> TCGA-06-0130-01A-01 2 0.0810 0.57243 0.000 0.976 0.008 0.004 0.004 0.008
#> TCGA-06-0139-01A-01 2 0.0810 0.57243 0.000 0.976 0.008 0.004 0.004 0.008
#> TCGA-06-0143-01A-01 1 0.4079 0.68421 0.760 0.004 0.096 0.000 0.000 0.140
#> TCGA-06-0147-01A-01 2 0.0810 0.57243 0.000 0.976 0.008 0.004 0.004 0.008
#> TCGA-06-0149-01A-05 6 0.5985 0.38288 0.004 0.184 0.096 0.000 0.092 0.624
#> TCGA-06-0152-01A-02 3 0.6793 0.48204 0.000 0.104 0.496 0.000 0.156 0.244
#> TCGA-06-0154-01A-02 2 0.3546 0.67895 0.004 0.788 0.020 0.000 0.008 0.180
#> TCGA-06-0164-01A-01 2 0.2544 0.67561 0.004 0.852 0.004 0.000 0.000 0.140
#> TCGA-06-0175-01A-01 2 0.4899 0.38220 0.036 0.588 0.020 0.000 0.000 0.356
#> TCGA-06-0176-01A-03 2 0.1814 0.66455 0.000 0.900 0.000 0.000 0.000 0.100
#> TCGA-06-0184-01A-01 6 0.5810 0.39521 0.000 0.180 0.032 0.012 0.144 0.632
#> TCGA-06-0189-01A-05 2 0.4381 0.07987 0.000 0.524 0.016 0.000 0.456 0.004
#> TCGA-06-0190-01A-01 2 0.3546 0.67895 0.004 0.788 0.020 0.000 0.008 0.180
#> TCGA-06-0194-01A-01 2 0.6168 0.46395 0.000 0.564 0.052 0.000 0.224 0.160
#> TCGA-06-0197-01A-02 2 0.4381 0.07987 0.000 0.524 0.016 0.000 0.456 0.004
#> TCGA-06-0210-01A-01 2 0.4191 0.65630 0.016 0.736 0.024 0.000 0.008 0.216
#> TCGA-06-0397-01A-01 2 0.3367 0.67154 0.020 0.804 0.012 0.000 0.000 0.164
#> TCGA-06-0409-01A-02 2 0.3259 0.66729 0.000 0.772 0.012 0.000 0.000 0.216
#> TCGA-06-0412-01A-01 2 0.4191 0.65630 0.016 0.736 0.024 0.000 0.008 0.216
#> TCGA-06-0644-01A-02 2 0.4374 0.09818 0.000 0.532 0.016 0.000 0.448 0.004
#> TCGA-06-0645-01A-01 2 0.6220 0.48736 0.012 0.560 0.064 0.012 0.048 0.304
#> TCGA-08-0346-01A-01 2 0.7330 0.20206 0.000 0.344 0.112 0.000 0.228 0.316
#> TCGA-08-0352-01A-01 2 0.6483 0.39890 0.020 0.516 0.048 0.028 0.040 0.348
#> TCGA-08-0360-01A-01 2 0.3852 0.65842 0.000 0.740 0.032 0.000 0.004 0.224
#> TCGA-08-0390-01A-01 6 0.7627 -0.19366 0.000 0.324 0.084 0.024 0.228 0.340
#> TCGA-08-0392-01A-01 5 0.4134 0.46376 0.000 0.240 0.052 0.000 0.708 0.000
#> TCGA-08-0509-01A-01 2 0.3950 0.63566 0.000 0.708 0.024 0.004 0.000 0.264
#> TCGA-08-0510-01A-01 1 0.5689 0.59070 0.596 0.036 0.088 0.000 0.004 0.276
#> TCGA-08-0512-01A-01 2 0.4002 0.61928 0.000 0.692 0.016 0.000 0.008 0.284
#> TCGA-08-0522-01A-01 2 0.2051 0.66507 0.004 0.896 0.004 0.000 0.000 0.096
#> TCGA-12-0619-01A-01 2 0.2053 0.66832 0.000 0.888 0.004 0.000 0.000 0.108
#> TCGA-12-0620-01A-01 2 0.7344 0.04933 0.000 0.324 0.108 0.000 0.320 0.248
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> CV:hclust 141 9.18e-14 2
#> CV:hclust 102 1.33e-28 3
#> CV:hclust 72 6.22e-12 4
#> CV:hclust 92 1.78e-17 5
#> CV:hclust 79 4.46e-18 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "kmeans"]
# you can also extract it by
# res = res_list["CV:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.722 0.883 0.944 0.4959 0.497 0.497
#> 3 3 0.381 0.421 0.664 0.3175 0.732 0.511
#> 4 4 0.458 0.531 0.728 0.1224 0.819 0.524
#> 5 5 0.557 0.517 0.696 0.0666 0.851 0.519
#> 6 6 0.664 0.620 0.772 0.0427 0.895 0.590
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.7219 0.79368 0.800 0.200
#> TCGA-02-0048-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0376 0.91238 0.996 0.004
#> TCGA-02-0069-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0376 0.91233 0.996 0.004
#> TCGA-02-0084-01A-03 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0087-01A-01 1 0.4022 0.87975 0.920 0.080
#> TCGA-02-0104-01A-01 2 0.2236 0.93486 0.036 0.964
#> TCGA-02-0114-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0321-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0325-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.4690 0.86711 0.900 0.100
#> TCGA-02-0439-01A-01 1 0.7056 0.79944 0.808 0.192
#> TCGA-02-0440-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.4161 0.87969 0.916 0.084
#> TCGA-06-0128-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.4022 0.88173 0.920 0.080
#> TCGA-06-0166-01A-01 2 0.0672 0.96150 0.008 0.992
#> TCGA-06-0174-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.6801 0.80751 0.820 0.180
#> TCGA-06-0238-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.7376 0.78035 0.792 0.208
#> TCGA-06-0413-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0646-01A-01 1 0.5408 0.85712 0.876 0.124
#> TCGA-06-0648-01A-01 2 0.2948 0.92081 0.052 0.948
#> TCGA-08-0245-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.9393 0.54719 0.644 0.356
#> TCGA-08-0347-01A-01 2 0.2948 0.91714 0.052 0.948
#> TCGA-08-0348-01A-01 1 0.4431 0.87542 0.908 0.092
#> TCGA-08-0350-01A-01 2 0.2043 0.93868 0.032 0.968
#> TCGA-08-0353-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.8713 0.66978 0.708 0.292
#> TCGA-08-0385-01A-01 2 0.2043 0.93868 0.032 0.968
#> TCGA-08-0517-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-12-0616-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-12-0618-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.8267 0.60927 0.260 0.740
#> TCGA-02-0115-01A-01 1 0.7528 0.77862 0.784 0.216
#> TCGA-02-0451-01A-01 1 0.9393 0.56804 0.644 0.356
#> TCGA-06-0132-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0138-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.9580 0.50435 0.620 0.380
#> TCGA-06-0162-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.9580 0.50435 0.620 0.380
#> TCGA-06-0171-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0173-01A-01 1 0.7299 0.79066 0.796 0.204
#> TCGA-06-0179-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0185-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.9286 0.57953 0.656 0.344
#> TCGA-06-0208-01B-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0221-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0237-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0240-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0349-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.4690 0.87106 0.900 0.100
#> TCGA-08-0520-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0007-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0009-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0016-01A-01 1 0.0376 0.91238 0.996 0.004
#> TCGA-02-0021-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0023-01B-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0038-01A-01 1 0.6048 0.84033 0.852 0.148
#> TCGA-02-0043-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0070-01A-01 1 0.9286 0.56075 0.656 0.344
#> TCGA-02-0102-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0260-01A-03 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0269-01B-01 2 0.9661 0.26181 0.392 0.608
#> TCGA-02-0285-01A-01 2 0.0376 0.96415 0.004 0.996
#> TCGA-02-0289-01A-01 1 0.9993 0.21883 0.516 0.484
#> TCGA-02-0290-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0317-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0333-01A-02 2 0.9710 0.23502 0.400 0.600
#> TCGA-02-0422-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0430-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0125-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0126-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0137-01A-03 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0145-01A-04 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0148-01A-01 1 0.0376 0.91225 0.996 0.004
#> TCGA-06-0187-01A-01 1 0.4939 0.86735 0.892 0.108
#> TCGA-06-0211-01B-01 1 0.9775 0.42617 0.588 0.412
#> TCGA-06-0402-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-08-0246-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0357-01A-01 2 0.3274 0.90800 0.060 0.940
#> TCGA-08-0358-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0375-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-08-0511-01A-01 1 0.7219 0.79254 0.800 0.200
#> TCGA-08-0514-01A-01 1 0.7815 0.76010 0.768 0.232
#> TCGA-08-0518-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-08-0529-01A-02 1 0.4815 0.86964 0.896 0.104
#> TCGA-08-0531-01A-01 1 0.9427 0.55784 0.640 0.360
#> TCGA-02-0057-01A-01 1 0.2603 0.89738 0.956 0.044
#> TCGA-02-0004-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.9970 -0.00206 0.468 0.532
#> TCGA-02-0025-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0376 0.96415 0.004 0.996
#> TCGA-02-0034-01A-01 2 0.0672 0.96122 0.008 0.992
#> TCGA-02-0039-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0054-01A-01 1 0.6438 0.82746 0.836 0.164
#> TCGA-02-0055-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0064-01A-01 1 0.2423 0.89878 0.960 0.040
#> TCGA-02-0075-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-02-0079-01A-03 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0376 0.96415 0.004 0.996
#> TCGA-02-0099-01A-01 1 0.7299 0.79197 0.796 0.204
#> TCGA-02-0106-01A-01 2 0.0376 0.96415 0.004 0.996
#> TCGA-02-0107-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-02-0337-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0122-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0124-01A-01 1 0.2423 0.89878 0.960 0.040
#> TCGA-06-0130-01A-01 2 0.0376 0.96415 0.004 0.996
#> TCGA-06-0139-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0143-01A-01 1 0.0000 0.91338 1.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0376 0.96415 0.004 0.996
#> TCGA-06-0164-01A-01 2 0.0672 0.96122 0.008 0.992
#> TCGA-06-0175-01A-01 1 0.5059 0.86474 0.888 0.112
#> TCGA-06-0176-01A-03 2 0.0376 0.96415 0.004 0.996
#> TCGA-06-0184-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0376 0.96415 0.004 0.996
#> TCGA-06-0397-01A-01 1 0.7056 0.79622 0.808 0.192
#> TCGA-06-0409-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.9044 0.49847 0.320 0.680
#> TCGA-06-0644-01A-02 2 0.0000 0.96635 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0672 0.96135 0.008 0.992
#> TCGA-08-0360-01A-01 2 0.0376 0.96415 0.004 0.996
#> TCGA-08-0390-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.96635 0.000 1.000
#> TCGA-08-0510-01A-01 1 0.2423 0.89878 0.960 0.040
#> TCGA-08-0512-01A-01 2 0.2236 0.93532 0.036 0.964
#> TCGA-08-0522-01A-01 2 0.1843 0.94370 0.028 0.972
#> TCGA-12-0619-01A-01 2 0.8861 0.52653 0.304 0.696
#> TCGA-12-0620-01A-01 2 0.0000 0.96635 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.1964 0.80753 0.944 0.000 0.056
#> TCGA-02-0010-01A-01 1 0.0000 0.81810 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0892 0.81736 0.980 0.000 0.020
#> TCGA-02-0014-01A-01 1 0.0237 0.81801 0.996 0.000 0.004
#> TCGA-02-0024-01B-01 1 0.1411 0.81452 0.964 0.000 0.036
#> TCGA-02-0026-01B-01 1 0.0592 0.81654 0.988 0.000 0.012
#> TCGA-02-0028-01A-01 1 0.0000 0.81810 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.81810 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 3 0.5111 0.44832 0.144 0.036 0.820
#> TCGA-02-0048-01A-01 1 0.2066 0.81337 0.940 0.000 0.060
#> TCGA-02-0060-01A-01 1 0.5835 0.47610 0.660 0.000 0.340
#> TCGA-02-0069-01A-01 1 0.0000 0.81810 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.81810 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.4784 0.67376 0.796 0.004 0.200
#> TCGA-02-0084-01A-03 2 0.5529 0.29799 0.000 0.704 0.296
#> TCGA-02-0087-01A-01 1 0.6487 0.53163 0.700 0.032 0.268
#> TCGA-02-0104-01A-01 3 0.8786 0.05131 0.112 0.424 0.464
#> TCGA-02-0114-01A-01 1 0.0237 0.81801 0.996 0.000 0.004
#> TCGA-02-0281-01A-01 1 0.0592 0.81654 0.988 0.000 0.012
#> TCGA-02-0321-01A-01 2 0.5591 0.27662 0.000 0.696 0.304
#> TCGA-02-0325-01A-01 1 0.0747 0.81745 0.984 0.000 0.016
#> TCGA-02-0338-01A-01 1 0.0237 0.81801 0.996 0.000 0.004
#> TCGA-02-0339-01A-01 1 0.0592 0.81654 0.988 0.000 0.012
#> TCGA-02-0432-01A-02 1 0.6113 0.52317 0.688 0.012 0.300
#> TCGA-02-0439-01A-01 3 0.6318 0.43713 0.172 0.068 0.760
#> TCGA-02-0440-01A-01 1 0.1529 0.81385 0.960 0.000 0.040
#> TCGA-02-0446-01A-01 3 0.6204 0.18096 0.424 0.000 0.576
#> TCGA-06-0128-01A-01 1 0.0000 0.81810 1.000 0.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.81810 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0424 0.81669 0.992 0.000 0.008
#> TCGA-06-0156-01A-01 1 0.7471 0.06782 0.516 0.036 0.448
#> TCGA-06-0166-01A-01 3 0.6608 -0.10765 0.008 0.432 0.560
#> TCGA-06-0174-01A-01 1 0.1964 0.80753 0.944 0.000 0.056
#> TCGA-06-0177-01A-01 1 0.7872 0.36595 0.620 0.084 0.296
#> TCGA-06-0238-01A-02 2 0.6215 0.12902 0.000 0.572 0.428
#> TCGA-06-0241-01A-02 1 0.1964 0.80753 0.944 0.000 0.056
#> TCGA-06-0410-01A-01 1 0.9825 -0.18881 0.388 0.244 0.368
#> TCGA-06-0413-01A-01 1 0.0424 0.81745 0.992 0.000 0.008
#> TCGA-06-0414-01A-01 1 0.1964 0.80753 0.944 0.000 0.056
#> TCGA-06-0646-01A-01 3 0.7637 0.38052 0.284 0.076 0.640
#> TCGA-06-0648-01A-01 2 0.8925 -0.06691 0.124 0.464 0.412
#> TCGA-08-0245-01A-01 1 0.1753 0.81095 0.952 0.000 0.048
#> TCGA-08-0344-01A-01 3 0.9149 0.07975 0.416 0.144 0.440
#> TCGA-08-0347-01A-01 3 0.4645 0.29897 0.008 0.176 0.816
#> TCGA-08-0348-01A-01 1 0.7640 0.22266 0.576 0.052 0.372
#> TCGA-08-0350-01A-01 2 0.8591 0.10927 0.128 0.572 0.300
#> TCGA-08-0353-01A-01 1 0.3816 0.78513 0.852 0.000 0.148
#> TCGA-08-0359-01A-01 3 0.8485 0.28143 0.224 0.164 0.612
#> TCGA-08-0385-01A-01 2 0.8333 0.09699 0.100 0.572 0.328
#> TCGA-08-0517-01A-01 1 0.1964 0.80902 0.944 0.000 0.056
#> TCGA-08-0524-01A-01 1 0.2066 0.80689 0.940 0.000 0.060
#> TCGA-12-0616-01A-01 2 0.5158 0.33496 0.004 0.764 0.232
#> TCGA-12-0618-01A-01 1 0.2165 0.80470 0.936 0.000 0.064
#> TCGA-02-0089-01A-01 3 0.2165 0.37527 0.000 0.064 0.936
#> TCGA-02-0113-01A-01 3 0.6633 0.33816 0.060 0.212 0.728
#> TCGA-02-0115-01A-01 3 0.2682 0.43319 0.076 0.004 0.920
#> TCGA-02-0451-01A-01 3 0.3589 0.41996 0.052 0.048 0.900
#> TCGA-06-0132-01A-02 3 0.6168 0.07724 0.000 0.412 0.588
#> TCGA-06-0133-01A-02 3 0.6192 0.08012 0.000 0.420 0.580
#> TCGA-06-0138-01A-02 2 0.6180 0.12560 0.000 0.584 0.416
#> TCGA-06-0160-01A-01 3 0.8650 0.25674 0.200 0.200 0.600
#> TCGA-06-0162-01A-01 2 0.6244 0.10825 0.000 0.560 0.440
#> TCGA-06-0167-01A-01 3 0.8650 0.25674 0.200 0.200 0.600
#> TCGA-06-0171-01A-02 3 0.6308 0.01021 0.000 0.492 0.508
#> TCGA-06-0173-01A-01 3 0.7493 0.41669 0.168 0.136 0.696
#> TCGA-06-0179-01A-02 3 0.6126 0.09338 0.000 0.400 0.600
#> TCGA-06-0182-01A-01 2 0.5363 0.27210 0.000 0.724 0.276
#> TCGA-06-0185-01A-01 3 0.5760 0.21730 0.000 0.328 0.672
#> TCGA-06-0195-01B-01 3 0.8746 0.23879 0.184 0.228 0.588
#> TCGA-06-0208-01B-01 3 0.6235 0.06620 0.000 0.436 0.564
#> TCGA-06-0214-01A-02 3 0.5785 0.07802 0.000 0.332 0.668
#> TCGA-06-0219-01A-01 2 0.6244 0.10825 0.000 0.560 0.440
#> TCGA-06-0221-01A-01 2 0.6235 0.11417 0.000 0.564 0.436
#> TCGA-06-0237-01A-02 2 0.6309 -0.03645 0.000 0.500 0.500
#> TCGA-06-0240-01A-02 3 0.6291 0.02768 0.000 0.468 0.532
#> TCGA-08-0349-01A-01 3 0.6307 0.01289 0.000 0.488 0.512
#> TCGA-08-0380-01A-01 3 0.6295 0.00179 0.000 0.472 0.528
#> TCGA-08-0386-01A-01 3 0.6819 0.27294 0.328 0.028 0.644
#> TCGA-08-0520-01A-01 2 0.6291 0.02861 0.000 0.532 0.468
#> TCGA-02-0007-01A-01 1 0.4931 0.72662 0.768 0.000 0.232
#> TCGA-02-0009-01A-01 1 0.3816 0.77656 0.852 0.000 0.148
#> TCGA-02-0016-01A-01 1 0.6260 0.41562 0.552 0.000 0.448
#> TCGA-02-0021-01A-01 1 0.4121 0.76068 0.832 0.000 0.168
#> TCGA-02-0023-01B-01 2 0.6095 0.15437 0.000 0.608 0.392
#> TCGA-02-0027-01A-01 1 0.3752 0.77932 0.856 0.000 0.144
#> TCGA-02-0038-01A-01 3 0.8122 0.39225 0.184 0.168 0.648
#> TCGA-02-0043-01A-01 1 0.3619 0.78276 0.864 0.000 0.136
#> TCGA-02-0070-01A-01 3 0.8627 0.06883 0.104 0.392 0.504
#> TCGA-02-0102-01A-01 1 0.3816 0.77656 0.852 0.000 0.148
#> TCGA-02-0260-01A-03 1 0.3551 0.78904 0.868 0.000 0.132
#> TCGA-02-0269-01B-01 3 0.8792 0.14719 0.112 0.432 0.456
#> TCGA-02-0285-01A-01 3 0.6235 -0.11823 0.000 0.436 0.564
#> TCGA-02-0289-01A-01 3 0.6646 0.36427 0.076 0.184 0.740
#> TCGA-02-0290-01A-01 2 0.3941 0.37868 0.000 0.844 0.156
#> TCGA-02-0317-01A-01 2 0.5529 0.28309 0.000 0.704 0.296
#> TCGA-02-0333-01A-02 3 0.8774 0.17213 0.112 0.412 0.476
#> TCGA-02-0422-01A-01 3 0.6033 0.11609 0.004 0.336 0.660
#> TCGA-02-0430-01A-01 1 0.4062 0.76388 0.836 0.000 0.164
#> TCGA-06-0125-01A-01 1 0.3619 0.78276 0.864 0.000 0.136
#> TCGA-06-0126-01A-01 1 0.3752 0.77932 0.856 0.000 0.144
#> TCGA-06-0137-01A-03 1 0.4062 0.77087 0.836 0.000 0.164
#> TCGA-06-0145-01A-04 1 0.5529 0.58678 0.704 0.000 0.296
#> TCGA-06-0148-01A-01 3 0.9616 0.23043 0.376 0.204 0.420
#> TCGA-06-0187-01A-01 3 0.8568 0.38119 0.228 0.168 0.604
#> TCGA-06-0211-01B-01 3 0.7821 0.38660 0.176 0.152 0.672
#> TCGA-06-0402-01A-01 1 0.3619 0.78226 0.864 0.000 0.136
#> TCGA-08-0246-01A-01 3 0.6295 -0.21558 0.000 0.472 0.528
#> TCGA-08-0354-01A-01 2 0.3879 0.38081 0.000 0.848 0.152
#> TCGA-08-0355-01A-01 2 0.6095 0.19498 0.000 0.608 0.392
#> TCGA-08-0357-01A-01 3 0.4749 0.33543 0.012 0.172 0.816
#> TCGA-08-0358-01A-01 2 0.5363 0.28883 0.000 0.724 0.276
#> TCGA-08-0375-01A-01 1 0.3752 0.78370 0.856 0.000 0.144
#> TCGA-08-0511-01A-01 3 0.5696 0.44489 0.148 0.056 0.796
#> TCGA-08-0514-01A-01 3 0.8153 0.35649 0.144 0.216 0.640
#> TCGA-08-0518-01A-01 1 0.3816 0.77656 0.852 0.000 0.148
#> TCGA-08-0529-01A-02 3 0.7979 0.40976 0.272 0.100 0.628
#> TCGA-08-0531-01A-01 3 0.6886 0.37252 0.088 0.184 0.728
#> TCGA-02-0057-01A-01 3 0.7581 0.13068 0.408 0.044 0.548
#> TCGA-02-0004-01A-01 2 0.5016 0.47251 0.000 0.760 0.240
#> TCGA-02-0006-01B-01 3 0.7807 0.20468 0.068 0.336 0.596
#> TCGA-02-0025-01A-01 2 0.0000 0.44826 0.000 1.000 0.000
#> TCGA-02-0033-01A-01 2 0.5760 0.45807 0.000 0.672 0.328
#> TCGA-02-0034-01A-01 2 0.5760 0.45807 0.000 0.672 0.328
#> TCGA-02-0039-01A-01 2 0.6062 0.41710 0.000 0.616 0.384
#> TCGA-02-0051-01A-01 2 0.0892 0.45288 0.000 0.980 0.020
#> TCGA-02-0054-01A-01 3 0.8345 0.28148 0.116 0.288 0.596
#> TCGA-02-0055-01A-01 2 0.3879 0.46999 0.000 0.848 0.152
#> TCGA-02-0059-01A-01 2 0.0000 0.44826 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 3 0.9546 0.26916 0.312 0.216 0.472
#> TCGA-02-0075-01A-01 1 0.7464 0.26942 0.560 0.040 0.400
#> TCGA-02-0079-01A-03 2 0.3752 0.37699 0.000 0.856 0.144
#> TCGA-02-0085-01A-01 3 0.5058 0.17026 0.000 0.244 0.756
#> TCGA-02-0086-01A-01 2 0.5859 0.44216 0.000 0.656 0.344
#> TCGA-02-0099-01A-01 3 0.8571 0.30468 0.140 0.272 0.588
#> TCGA-02-0106-01A-01 2 0.5760 0.45807 0.000 0.672 0.328
#> TCGA-02-0107-01A-01 2 0.5733 0.45912 0.000 0.676 0.324
#> TCGA-02-0111-01A-01 2 0.2625 0.46334 0.000 0.916 0.084
#> TCGA-02-0326-01A-01 2 0.5591 0.26531 0.000 0.696 0.304
#> TCGA-02-0337-01A-01 2 0.5678 0.46686 0.000 0.684 0.316
#> TCGA-06-0122-01A-01 1 0.5291 0.63238 0.732 0.000 0.268
#> TCGA-06-0124-01A-01 1 0.8637 -0.02256 0.456 0.100 0.444
#> TCGA-06-0130-01A-01 2 0.5760 0.45807 0.000 0.672 0.328
#> TCGA-06-0139-01A-01 2 0.5621 0.46739 0.000 0.692 0.308
#> TCGA-06-0143-01A-01 1 0.5016 0.67361 0.760 0.000 0.240
#> TCGA-06-0147-01A-01 2 0.5760 0.45807 0.000 0.672 0.328
#> TCGA-06-0149-01A-05 2 0.6045 0.40773 0.000 0.620 0.380
#> TCGA-06-0152-01A-02 2 0.4605 0.34833 0.000 0.796 0.204
#> TCGA-06-0154-01A-02 2 0.5760 0.45807 0.000 0.672 0.328
#> TCGA-06-0164-01A-01 2 0.5835 0.44615 0.000 0.660 0.340
#> TCGA-06-0175-01A-01 3 0.7864 0.27272 0.332 0.072 0.596
#> TCGA-06-0176-01A-03 2 0.5760 0.45807 0.000 0.672 0.328
#> TCGA-06-0184-01A-01 2 0.6260 0.31065 0.000 0.552 0.448
#> TCGA-06-0189-01A-05 2 0.0237 0.44949 0.000 0.996 0.004
#> TCGA-06-0190-01A-01 2 0.5760 0.45807 0.000 0.672 0.328
#> TCGA-06-0194-01A-01 2 0.5621 0.46739 0.000 0.692 0.308
#> TCGA-06-0197-01A-02 2 0.3752 0.46961 0.000 0.856 0.144
#> TCGA-06-0210-01A-01 2 0.5760 0.45807 0.000 0.672 0.328
#> TCGA-06-0397-01A-01 2 0.7672 0.10675 0.044 0.488 0.468
#> TCGA-06-0409-01A-02 2 0.5835 0.44615 0.000 0.660 0.340
#> TCGA-06-0412-01A-01 2 0.6299 0.17950 0.000 0.524 0.476
#> TCGA-06-0644-01A-02 2 0.5216 0.47262 0.000 0.740 0.260
#> TCGA-06-0645-01A-01 2 0.5650 0.46603 0.000 0.688 0.312
#> TCGA-08-0346-01A-01 2 0.5291 0.47197 0.000 0.732 0.268
#> TCGA-08-0352-01A-01 3 0.5465 0.20406 0.000 0.288 0.712
#> TCGA-08-0360-01A-01 2 0.5760 0.45807 0.000 0.672 0.328
#> TCGA-08-0390-01A-01 2 0.5254 0.29689 0.000 0.736 0.264
#> TCGA-08-0392-01A-01 2 0.0747 0.44272 0.000 0.984 0.016
#> TCGA-08-0509-01A-01 2 0.5948 0.41958 0.000 0.640 0.360
#> TCGA-08-0510-01A-01 3 0.7996 -0.01910 0.464 0.060 0.476
#> TCGA-08-0512-01A-01 2 0.5859 0.44156 0.000 0.656 0.344
#> TCGA-08-0522-01A-01 2 0.5785 0.45351 0.000 0.668 0.332
#> TCGA-12-0619-01A-01 2 0.6033 0.44303 0.004 0.660 0.336
#> TCGA-12-0620-01A-01 2 0.2066 0.43720 0.000 0.940 0.060
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.2589 0.7139 0.884 0.000 0.116 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.7380 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.1792 0.7328 0.932 0.000 0.068 0.000
#> TCGA-02-0014-01A-01 1 0.0592 0.7401 0.984 0.000 0.016 0.000
#> TCGA-02-0024-01B-01 1 0.2149 0.7263 0.912 0.000 0.088 0.000
#> TCGA-02-0026-01B-01 1 0.0921 0.7385 0.972 0.000 0.028 0.000
#> TCGA-02-0028-01A-01 1 0.0336 0.7371 0.992 0.000 0.008 0.000
#> TCGA-02-0046-01A-01 1 0.0592 0.7401 0.984 0.000 0.016 0.000
#> TCGA-02-0047-01A-01 3 0.6343 0.6136 0.032 0.184 0.700 0.084
#> TCGA-02-0048-01A-01 1 0.3356 0.6943 0.824 0.000 0.176 0.000
#> TCGA-02-0060-01A-01 3 0.5861 -0.1226 0.476 0.000 0.492 0.032
#> TCGA-02-0069-01A-01 1 0.0188 0.7375 0.996 0.000 0.004 0.000
#> TCGA-02-0074-01A-01 1 0.0336 0.7371 0.992 0.000 0.008 0.000
#> TCGA-02-0080-01A-01 1 0.5154 0.4748 0.660 0.004 0.324 0.012
#> TCGA-02-0084-01A-03 4 0.7392 0.5204 0.000 0.232 0.248 0.520
#> TCGA-02-0087-01A-01 1 0.6599 0.1630 0.500 0.020 0.440 0.040
#> TCGA-02-0104-01A-01 4 0.3400 0.6393 0.044 0.004 0.076 0.876
#> TCGA-02-0114-01A-01 1 0.0592 0.7401 0.984 0.000 0.016 0.000
#> TCGA-02-0281-01A-01 1 0.0921 0.7385 0.972 0.000 0.028 0.000
#> TCGA-02-0321-01A-01 4 0.6704 0.5669 0.000 0.136 0.264 0.600
#> TCGA-02-0325-01A-01 1 0.2412 0.7221 0.908 0.000 0.084 0.008
#> TCGA-02-0338-01A-01 1 0.0592 0.7401 0.984 0.000 0.016 0.000
#> TCGA-02-0339-01A-01 1 0.0921 0.7385 0.972 0.000 0.028 0.000
#> TCGA-02-0432-01A-02 1 0.5602 0.3155 0.568 0.000 0.408 0.024
#> TCGA-02-0439-01A-01 3 0.4781 0.5846 0.024 0.104 0.812 0.060
#> TCGA-02-0440-01A-01 1 0.2530 0.7156 0.888 0.000 0.112 0.000
#> TCGA-02-0446-01A-01 3 0.7643 0.5565 0.200 0.176 0.588 0.036
#> TCGA-06-0128-01A-01 1 0.0524 0.7365 0.988 0.000 0.008 0.004
#> TCGA-06-0129-01A-01 1 0.0524 0.7365 0.988 0.000 0.008 0.004
#> TCGA-06-0146-01A-01 1 0.0707 0.7359 0.980 0.000 0.020 0.000
#> TCGA-06-0156-01A-01 3 0.7916 0.5176 0.272 0.232 0.484 0.012
#> TCGA-06-0166-01A-01 3 0.6602 0.4515 0.020 0.444 0.496 0.040
#> TCGA-06-0174-01A-01 1 0.2530 0.7156 0.888 0.000 0.112 0.000
#> TCGA-06-0177-01A-01 1 0.7575 0.2997 0.536 0.012 0.272 0.180
#> TCGA-06-0238-01A-02 4 0.2021 0.6427 0.000 0.012 0.056 0.932
#> TCGA-06-0241-01A-02 1 0.2530 0.7156 0.888 0.000 0.112 0.000
#> TCGA-06-0410-01A-01 1 0.8128 -0.0637 0.384 0.008 0.272 0.336
#> TCGA-06-0413-01A-01 1 0.0592 0.7401 0.984 0.000 0.016 0.000
#> TCGA-06-0414-01A-01 1 0.2530 0.7156 0.888 0.000 0.112 0.000
#> TCGA-06-0646-01A-01 3 0.6124 0.6582 0.068 0.288 0.640 0.004
#> TCGA-06-0648-01A-01 4 0.6103 0.5612 0.076 0.004 0.264 0.656
#> TCGA-08-0245-01A-01 1 0.2408 0.7192 0.896 0.000 0.104 0.000
#> TCGA-08-0344-01A-01 1 0.7392 0.1595 0.460 0.000 0.372 0.168
#> TCGA-08-0347-01A-01 3 0.5658 0.5364 0.008 0.156 0.736 0.100
#> TCGA-08-0348-01A-01 3 0.6494 0.0778 0.432 0.040 0.512 0.016
#> TCGA-08-0350-01A-01 4 0.8353 0.4500 0.152 0.060 0.284 0.504
#> TCGA-08-0353-01A-01 1 0.5244 0.4913 0.600 0.012 0.388 0.000
#> TCGA-08-0359-01A-01 3 0.6973 -0.0812 0.116 0.012 0.596 0.276
#> TCGA-08-0385-01A-01 4 0.6560 0.5877 0.056 0.048 0.224 0.672
#> TCGA-08-0517-01A-01 1 0.3710 0.6495 0.804 0.004 0.192 0.000
#> TCGA-08-0524-01A-01 1 0.2647 0.7136 0.880 0.000 0.120 0.000
#> TCGA-12-0616-01A-01 4 0.6787 0.5898 0.060 0.064 0.208 0.668
#> TCGA-12-0618-01A-01 1 0.2973 0.7012 0.856 0.000 0.144 0.000
#> TCGA-02-0089-01A-01 3 0.6690 0.5171 0.000 0.188 0.620 0.192
#> TCGA-02-0113-01A-01 3 0.5848 0.6370 0.008 0.320 0.636 0.036
#> TCGA-02-0115-01A-01 3 0.6553 0.4596 0.008 0.136 0.656 0.200
#> TCGA-02-0451-01A-01 3 0.6431 0.5998 0.008 0.208 0.664 0.120
#> TCGA-06-0132-01A-02 4 0.6179 0.3464 0.000 0.056 0.392 0.552
#> TCGA-06-0133-01A-02 4 0.5476 0.3811 0.000 0.020 0.396 0.584
#> TCGA-06-0138-01A-02 4 0.2255 0.6408 0.000 0.012 0.068 0.920
#> TCGA-06-0160-01A-01 4 0.6936 0.3034 0.076 0.012 0.416 0.496
#> TCGA-06-0162-01A-01 4 0.1610 0.6294 0.000 0.016 0.032 0.952
#> TCGA-06-0167-01A-01 4 0.6936 0.3034 0.076 0.012 0.416 0.496
#> TCGA-06-0171-01A-02 4 0.4621 0.5300 0.000 0.008 0.284 0.708
#> TCGA-06-0173-01A-01 3 0.6510 0.6581 0.036 0.284 0.636 0.044
#> TCGA-06-0179-01A-02 4 0.6349 0.3420 0.004 0.056 0.392 0.548
#> TCGA-06-0182-01A-01 4 0.3687 0.6417 0.000 0.080 0.064 0.856
#> TCGA-06-0185-01A-01 4 0.6094 0.3169 0.000 0.048 0.416 0.536
#> TCGA-06-0195-01B-01 4 0.6742 0.3213 0.072 0.008 0.400 0.520
#> TCGA-06-0208-01B-01 4 0.6042 0.3611 0.000 0.048 0.392 0.560
#> TCGA-06-0214-01A-02 3 0.6746 0.5772 0.000 0.340 0.552 0.108
#> TCGA-06-0219-01A-01 4 0.1706 0.6306 0.000 0.016 0.036 0.948
#> TCGA-06-0221-01A-01 4 0.1610 0.6294 0.000 0.016 0.032 0.952
#> TCGA-06-0237-01A-02 4 0.4088 0.5779 0.000 0.004 0.232 0.764
#> TCGA-06-0240-01A-02 4 0.4328 0.5415 0.000 0.008 0.244 0.748
#> TCGA-08-0349-01A-01 4 0.4872 0.5224 0.000 0.004 0.356 0.640
#> TCGA-08-0380-01A-01 4 0.6863 0.3216 0.000 0.116 0.348 0.536
#> TCGA-08-0386-01A-01 3 0.5489 0.6399 0.088 0.128 0.764 0.020
#> TCGA-08-0520-01A-01 4 0.4175 0.6078 0.000 0.016 0.200 0.784
#> TCGA-02-0007-01A-01 3 0.6116 0.2456 0.320 0.068 0.612 0.000
#> TCGA-02-0009-01A-01 1 0.5352 0.5593 0.676 0.020 0.296 0.008
#> TCGA-02-0016-01A-01 3 0.4181 0.5322 0.136 0.032 0.824 0.008
#> TCGA-02-0021-01A-01 1 0.5891 0.4725 0.612 0.032 0.348 0.008
#> TCGA-02-0023-01B-01 4 0.5235 0.6167 0.000 0.048 0.236 0.716
#> TCGA-02-0027-01A-01 1 0.5375 0.5578 0.672 0.020 0.300 0.008
#> TCGA-02-0038-01A-01 3 0.5881 0.6450 0.044 0.296 0.652 0.008
#> TCGA-02-0043-01A-01 1 0.5352 0.5593 0.676 0.020 0.296 0.008
#> TCGA-02-0070-01A-01 3 0.5577 0.5403 0.016 0.364 0.612 0.008
#> TCGA-02-0102-01A-01 1 0.5352 0.5593 0.676 0.020 0.296 0.008
#> TCGA-02-0260-01A-03 1 0.5326 0.5818 0.668 0.012 0.308 0.012
#> TCGA-02-0269-01B-01 3 0.6268 -0.2122 0.000 0.056 0.496 0.448
#> TCGA-02-0285-01A-01 3 0.7373 0.4125 0.000 0.300 0.508 0.192
#> TCGA-02-0289-01A-01 3 0.4992 0.5786 0.000 0.132 0.772 0.096
#> TCGA-02-0290-01A-01 4 0.6233 0.5431 0.000 0.216 0.124 0.660
#> TCGA-02-0317-01A-01 4 0.6107 0.5662 0.000 0.088 0.264 0.648
#> TCGA-02-0333-01A-02 3 0.6168 -0.0300 0.000 0.056 0.556 0.388
#> TCGA-02-0422-01A-01 3 0.5894 0.5622 0.000 0.200 0.692 0.108
#> TCGA-02-0430-01A-01 1 0.5884 0.4486 0.580 0.032 0.384 0.004
#> TCGA-06-0125-01A-01 1 0.5352 0.5593 0.676 0.020 0.296 0.008
#> TCGA-06-0126-01A-01 1 0.5352 0.5593 0.676 0.020 0.296 0.008
#> TCGA-06-0137-01A-03 3 0.5811 -0.0365 0.408 0.020 0.564 0.008
#> TCGA-06-0145-01A-04 1 0.7353 0.1299 0.468 0.124 0.400 0.008
#> TCGA-06-0148-01A-01 3 0.7812 0.4410 0.208 0.312 0.472 0.008
#> TCGA-06-0187-01A-01 3 0.5764 0.6353 0.052 0.304 0.644 0.000
#> TCGA-06-0211-01B-01 3 0.6476 0.5944 0.076 0.096 0.720 0.108
#> TCGA-06-0402-01A-01 1 0.5352 0.5593 0.676 0.020 0.296 0.008
#> TCGA-08-0246-01A-01 3 0.6686 0.4614 0.000 0.388 0.520 0.092
#> TCGA-08-0354-01A-01 4 0.5998 0.5189 0.000 0.240 0.092 0.668
#> TCGA-08-0355-01A-01 4 0.7040 0.3505 0.000 0.120 0.420 0.460
#> TCGA-08-0357-01A-01 3 0.5266 0.5707 0.000 0.140 0.752 0.108
#> TCGA-08-0358-01A-01 4 0.5906 0.6022 0.000 0.152 0.148 0.700
#> TCGA-08-0375-01A-01 1 0.5537 0.4415 0.544 0.012 0.440 0.004
#> TCGA-08-0511-01A-01 3 0.4698 0.6628 0.032 0.180 0.780 0.008
#> TCGA-08-0514-01A-01 3 0.5207 0.6490 0.028 0.292 0.680 0.000
#> TCGA-08-0518-01A-01 1 0.5464 0.5349 0.656 0.020 0.316 0.008
#> TCGA-08-0529-01A-02 3 0.5256 0.6530 0.036 0.272 0.692 0.000
#> TCGA-08-0531-01A-01 3 0.5337 0.6689 0.020 0.244 0.716 0.020
#> TCGA-02-0057-01A-01 3 0.6918 0.5911 0.124 0.296 0.576 0.004
#> TCGA-02-0004-01A-01 2 0.3157 0.6927 0.000 0.852 0.004 0.144
#> TCGA-02-0006-01B-01 3 0.5163 0.4538 0.004 0.480 0.516 0.000
#> TCGA-02-0025-01A-01 2 0.5742 0.2892 0.000 0.596 0.036 0.368
#> TCGA-02-0033-01A-01 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.5356 0.5205 0.000 0.728 0.200 0.072
#> TCGA-02-0051-01A-01 2 0.5167 0.3897 0.000 0.644 0.016 0.340
#> TCGA-02-0054-01A-01 3 0.5383 0.4998 0.012 0.452 0.536 0.000
#> TCGA-02-0055-01A-01 2 0.3626 0.6501 0.000 0.812 0.004 0.184
#> TCGA-02-0059-01A-01 2 0.5364 0.2785 0.000 0.592 0.016 0.392
#> TCGA-02-0064-01A-01 2 0.7003 -0.0558 0.112 0.564 0.316 0.008
#> TCGA-02-0075-01A-01 2 0.8193 -0.2840 0.324 0.348 0.320 0.008
#> TCGA-02-0079-01A-03 4 0.6831 0.3175 0.000 0.352 0.112 0.536
#> TCGA-02-0085-01A-01 3 0.7582 0.2066 0.000 0.336 0.456 0.208
#> TCGA-02-0086-01A-01 2 0.0817 0.7523 0.000 0.976 0.024 0.000
#> TCGA-02-0099-01A-01 3 0.5607 0.4419 0.020 0.484 0.496 0.000
#> TCGA-02-0106-01A-01 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0524 0.7658 0.000 0.988 0.008 0.004
#> TCGA-02-0111-01A-01 2 0.4826 0.5132 0.000 0.716 0.020 0.264
#> TCGA-02-0326-01A-01 4 0.5434 0.6186 0.000 0.128 0.132 0.740
#> TCGA-02-0337-01A-01 2 0.5578 0.5673 0.000 0.728 0.128 0.144
#> TCGA-06-0122-01A-01 1 0.7094 0.3637 0.556 0.120 0.316 0.008
#> TCGA-06-0124-01A-01 2 0.8040 -0.2847 0.240 0.404 0.348 0.008
#> TCGA-06-0130-01A-01 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0817 0.7639 0.000 0.976 0.000 0.024
#> TCGA-06-0143-01A-01 1 0.6913 0.4210 0.584 0.112 0.296 0.008
#> TCGA-06-0147-01A-01 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.4663 0.3546 0.000 0.716 0.272 0.012
#> TCGA-06-0152-01A-02 4 0.6388 0.5646 0.000 0.192 0.156 0.652
#> TCGA-06-0154-01A-02 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.6334 0.6260 0.080 0.328 0.592 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.5496 0.3876 0.000 0.704 0.232 0.064
#> TCGA-06-0189-01A-05 2 0.5352 0.2885 0.000 0.596 0.016 0.388
#> TCGA-06-0190-01A-01 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0895 0.7640 0.000 0.976 0.004 0.020
#> TCGA-06-0197-01A-02 2 0.3751 0.6350 0.000 0.800 0.004 0.196
#> TCGA-06-0210-01A-01 2 0.0469 0.7602 0.000 0.988 0.012 0.000
#> TCGA-06-0397-01A-01 2 0.4012 0.4828 0.016 0.800 0.184 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.4331 0.2226 0.000 0.712 0.288 0.000
#> TCGA-06-0644-01A-02 2 0.2999 0.7036 0.000 0.864 0.004 0.132
#> TCGA-06-0645-01A-01 2 0.1913 0.7507 0.000 0.940 0.020 0.040
#> TCGA-08-0346-01A-01 2 0.4949 0.6028 0.000 0.760 0.060 0.180
#> TCGA-08-0352-01A-01 3 0.4891 0.6331 0.000 0.308 0.680 0.012
#> TCGA-08-0360-01A-01 2 0.0336 0.7676 0.000 0.992 0.008 0.000
#> TCGA-08-0390-01A-01 4 0.5631 0.5280 0.000 0.232 0.072 0.696
#> TCGA-08-0392-01A-01 4 0.5688 0.0502 0.000 0.464 0.024 0.512
#> TCGA-08-0509-01A-01 2 0.0188 0.7666 0.000 0.996 0.004 0.000
#> TCGA-08-0510-01A-01 3 0.7873 0.4219 0.208 0.336 0.448 0.008
#> TCGA-08-0512-01A-01 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.7691 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0336 0.7635 0.000 0.992 0.008 0.000
#> TCGA-12-0620-01A-01 4 0.6968 0.2194 0.000 0.392 0.116 0.492
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.3693 0.78147 0.836 0.000 0.104 0.036 0.024
#> TCGA-02-0010-01A-01 1 0.0324 0.79871 0.992 0.000 0.004 0.004 0.000
#> TCGA-02-0011-01B-01 1 0.2100 0.80339 0.924 0.000 0.048 0.016 0.012
#> TCGA-02-0014-01A-01 1 0.0000 0.80160 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.2800 0.79795 0.888 0.000 0.072 0.024 0.016
#> TCGA-02-0026-01B-01 1 0.0324 0.80211 0.992 0.000 0.004 0.000 0.004
#> TCGA-02-0028-01A-01 1 0.0324 0.79871 0.992 0.000 0.004 0.004 0.000
#> TCGA-02-0046-01A-01 1 0.0162 0.80215 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0047-01A-01 3 0.7633 0.16757 0.008 0.104 0.456 0.332 0.100
#> TCGA-02-0048-01A-01 1 0.4556 0.70347 0.756 0.000 0.184 0.028 0.032
#> TCGA-02-0060-01A-01 1 0.6768 0.49001 0.556 0.000 0.140 0.260 0.044
#> TCGA-02-0069-01A-01 1 0.0324 0.79871 0.992 0.000 0.004 0.004 0.000
#> TCGA-02-0074-01A-01 1 0.0807 0.79065 0.976 0.000 0.012 0.012 0.000
#> TCGA-02-0080-01A-01 1 0.6850 0.46344 0.568 0.000 0.216 0.052 0.164
#> TCGA-02-0084-01A-03 5 0.4426 0.59936 0.000 0.056 0.128 0.028 0.788
#> TCGA-02-0087-01A-01 5 0.7787 0.10431 0.316 0.004 0.248 0.052 0.380
#> TCGA-02-0104-01A-01 5 0.4434 0.45139 0.020 0.000 0.012 0.248 0.720
#> TCGA-02-0114-01A-01 1 0.0000 0.80160 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0451 0.80268 0.988 0.000 0.008 0.000 0.004
#> TCGA-02-0321-01A-01 5 0.3592 0.58855 0.000 0.028 0.124 0.016 0.832
#> TCGA-02-0325-01A-01 1 0.5096 0.35770 0.636 0.000 0.320 0.024 0.020
#> TCGA-02-0338-01A-01 1 0.0000 0.80160 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0324 0.80211 0.992 0.000 0.004 0.000 0.004
#> TCGA-02-0432-01A-02 1 0.7057 0.46488 0.560 0.000 0.200 0.072 0.168
#> TCGA-02-0439-01A-01 3 0.7399 0.10513 0.004 0.032 0.440 0.228 0.296
#> TCGA-02-0440-01A-01 1 0.3522 0.78523 0.844 0.000 0.104 0.032 0.020
#> TCGA-02-0446-01A-01 3 0.8776 0.09885 0.176 0.092 0.388 0.288 0.056
#> TCGA-06-0128-01A-01 1 0.1630 0.77697 0.944 0.000 0.036 0.016 0.004
#> TCGA-06-0129-01A-01 1 0.1597 0.76544 0.940 0.000 0.048 0.012 0.000
#> TCGA-06-0146-01A-01 1 0.1369 0.78936 0.956 0.000 0.028 0.008 0.008
#> TCGA-06-0156-01A-01 3 0.9115 0.19881 0.168 0.160 0.392 0.216 0.064
#> TCGA-06-0166-01A-01 3 0.8319 0.13518 0.000 0.260 0.372 0.204 0.164
#> TCGA-06-0174-01A-01 1 0.3522 0.78523 0.844 0.000 0.104 0.032 0.020
#> TCGA-06-0177-01A-01 1 0.6195 0.58925 0.632 0.000 0.148 0.032 0.188
#> TCGA-06-0238-01A-02 5 0.3086 0.53492 0.000 0.004 0.000 0.180 0.816
#> TCGA-06-0241-01A-02 1 0.3522 0.78523 0.844 0.000 0.104 0.032 0.020
#> TCGA-06-0410-01A-01 1 0.7088 0.50609 0.568 0.000 0.200 0.132 0.100
#> TCGA-06-0413-01A-01 1 0.0000 0.80160 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.3248 0.79257 0.864 0.000 0.084 0.032 0.020
#> TCGA-06-0646-01A-01 3 0.8179 0.29811 0.032 0.132 0.488 0.116 0.232
#> TCGA-06-0648-01A-01 5 0.3846 0.57945 0.036 0.000 0.132 0.016 0.816
#> TCGA-08-0245-01A-01 1 0.3455 0.78308 0.844 0.000 0.112 0.024 0.020
#> TCGA-08-0344-01A-01 1 0.7241 0.46139 0.536 0.000 0.208 0.076 0.180
#> TCGA-08-0347-01A-01 3 0.7992 0.00942 0.004 0.068 0.364 0.272 0.292
#> TCGA-08-0348-01A-01 1 0.7551 0.26639 0.428 0.000 0.284 0.052 0.236
#> TCGA-08-0350-01A-01 5 0.4579 0.56466 0.048 0.004 0.148 0.024 0.776
#> TCGA-08-0353-01A-01 1 0.5632 0.08002 0.480 0.000 0.464 0.020 0.036
#> TCGA-08-0359-01A-01 4 0.7124 0.38396 0.036 0.008 0.192 0.536 0.228
#> TCGA-08-0385-01A-01 5 0.2606 0.61803 0.032 0.000 0.056 0.012 0.900
#> TCGA-08-0517-01A-01 1 0.4611 0.69192 0.744 0.000 0.200 0.028 0.028
#> TCGA-08-0524-01A-01 1 0.3278 0.79303 0.860 0.000 0.092 0.028 0.020
#> TCGA-12-0616-01A-01 5 0.3340 0.59599 0.044 0.000 0.088 0.012 0.856
#> TCGA-12-0618-01A-01 1 0.3426 0.79271 0.856 0.000 0.084 0.032 0.028
#> TCGA-02-0089-01A-01 3 0.7229 0.01000 0.000 0.100 0.412 0.408 0.080
#> TCGA-02-0113-01A-01 3 0.7031 0.37103 0.000 0.156 0.572 0.188 0.084
#> TCGA-02-0115-01A-01 4 0.5370 0.41272 0.000 0.028 0.256 0.668 0.048
#> TCGA-02-0451-01A-01 3 0.7436 0.13403 0.004 0.104 0.456 0.348 0.088
#> TCGA-06-0132-01A-02 4 0.2086 0.67557 0.000 0.008 0.020 0.924 0.048
#> TCGA-06-0133-01A-02 4 0.2321 0.67079 0.000 0.008 0.024 0.912 0.056
#> TCGA-06-0138-01A-02 5 0.4508 0.32286 0.000 0.000 0.020 0.332 0.648
#> TCGA-06-0160-01A-01 4 0.1996 0.67369 0.004 0.008 0.016 0.932 0.040
#> TCGA-06-0162-01A-01 5 0.4572 0.16773 0.000 0.004 0.004 0.452 0.540
#> TCGA-06-0167-01A-01 4 0.1996 0.67369 0.004 0.008 0.016 0.932 0.040
#> TCGA-06-0171-01A-02 4 0.6128 0.31137 0.000 0.004 0.116 0.500 0.380
#> TCGA-06-0173-01A-01 3 0.7610 0.29711 0.012 0.140 0.520 0.240 0.088
#> TCGA-06-0179-01A-02 4 0.2086 0.67557 0.000 0.008 0.020 0.924 0.048
#> TCGA-06-0182-01A-01 5 0.5046 0.36949 0.000 0.020 0.028 0.292 0.660
#> TCGA-06-0185-01A-01 4 0.7215 0.42765 0.000 0.036 0.272 0.472 0.220
#> TCGA-06-0195-01B-01 4 0.2094 0.67563 0.004 0.008 0.020 0.928 0.040
#> TCGA-06-0208-01B-01 4 0.6383 0.53995 0.000 0.024 0.208 0.596 0.172
#> TCGA-06-0214-01A-02 3 0.7912 0.16413 0.000 0.172 0.428 0.284 0.116
#> TCGA-06-0219-01A-01 5 0.4567 0.17569 0.000 0.004 0.004 0.448 0.544
#> TCGA-06-0221-01A-01 5 0.4562 0.18404 0.000 0.004 0.004 0.444 0.548
#> TCGA-06-0237-01A-02 4 0.6164 0.18743 0.000 0.004 0.116 0.472 0.408
#> TCGA-06-0240-01A-02 4 0.2329 0.56840 0.000 0.000 0.000 0.876 0.124
#> TCGA-08-0349-01A-01 5 0.6426 0.04741 0.000 0.012 0.148 0.308 0.532
#> TCGA-08-0380-01A-01 4 0.7653 0.30505 0.000 0.068 0.196 0.416 0.320
#> TCGA-08-0386-01A-01 3 0.6409 0.38247 0.020 0.048 0.656 0.184 0.092
#> TCGA-08-0520-01A-01 5 0.5715 0.07016 0.000 0.004 0.088 0.332 0.576
#> TCGA-02-0007-01A-01 3 0.4925 0.48589 0.064 0.024 0.788 0.080 0.044
#> TCGA-02-0009-01A-01 3 0.4859 0.31666 0.364 0.004 0.608 0.024 0.000
#> TCGA-02-0016-01A-01 3 0.4292 0.44567 0.008 0.008 0.796 0.060 0.128
#> TCGA-02-0021-01A-01 3 0.4414 0.44420 0.248 0.008 0.720 0.024 0.000
#> TCGA-02-0023-01B-01 5 0.3556 0.59676 0.000 0.012 0.116 0.036 0.836
#> TCGA-02-0027-01A-01 3 0.4949 0.30961 0.368 0.004 0.600 0.028 0.000
#> TCGA-02-0038-01A-01 3 0.6094 0.45503 0.004 0.148 0.676 0.116 0.056
#> TCGA-02-0043-01A-01 3 0.4883 0.30501 0.372 0.004 0.600 0.024 0.000
#> TCGA-02-0070-01A-01 3 0.6235 0.33749 0.000 0.128 0.576 0.016 0.280
#> TCGA-02-0102-01A-01 3 0.4859 0.31666 0.364 0.004 0.608 0.024 0.000
#> TCGA-02-0260-01A-03 3 0.7158 0.21261 0.292 0.004 0.472 0.024 0.208
#> TCGA-02-0269-01B-01 5 0.4610 0.46257 0.000 0.008 0.296 0.020 0.676
#> TCGA-02-0285-01A-01 5 0.6441 -0.02083 0.000 0.104 0.428 0.020 0.448
#> TCGA-02-0289-01A-01 3 0.5851 0.16397 0.000 0.028 0.552 0.048 0.372
#> TCGA-02-0290-01A-01 5 0.1942 0.62199 0.000 0.068 0.000 0.012 0.920
#> TCGA-02-0317-01A-01 5 0.3044 0.60405 0.000 0.008 0.148 0.004 0.840
#> TCGA-02-0333-01A-02 5 0.4904 0.37426 0.000 0.008 0.368 0.020 0.604
#> TCGA-02-0422-01A-01 3 0.7206 0.27734 0.000 0.084 0.504 0.112 0.300
#> TCGA-02-0430-01A-01 3 0.4004 0.47072 0.232 0.004 0.748 0.000 0.016
#> TCGA-06-0125-01A-01 3 0.4883 0.30501 0.372 0.004 0.600 0.024 0.000
#> TCGA-06-0126-01A-01 3 0.4883 0.30501 0.372 0.004 0.600 0.024 0.000
#> TCGA-06-0137-01A-03 3 0.3880 0.48285 0.184 0.004 0.784 0.028 0.000
#> TCGA-06-0145-01A-04 3 0.4528 0.48225 0.200 0.028 0.748 0.024 0.000
#> TCGA-06-0148-01A-01 3 0.4368 0.48141 0.040 0.076 0.820 0.020 0.044
#> TCGA-06-0187-01A-01 3 0.5645 0.47855 0.004 0.148 0.712 0.084 0.052
#> TCGA-06-0211-01B-01 3 0.6605 0.32488 0.004 0.044 0.608 0.200 0.144
#> TCGA-06-0402-01A-01 3 0.4832 0.32584 0.356 0.004 0.616 0.024 0.000
#> TCGA-08-0246-01A-01 3 0.7964 0.20556 0.000 0.192 0.396 0.104 0.308
#> TCGA-08-0354-01A-01 5 0.2448 0.61180 0.000 0.088 0.000 0.020 0.892
#> TCGA-08-0355-01A-01 5 0.5648 0.41000 0.000 0.036 0.212 0.076 0.676
#> TCGA-08-0357-01A-01 3 0.7125 0.24873 0.000 0.056 0.508 0.148 0.288
#> TCGA-08-0358-01A-01 5 0.1830 0.62645 0.000 0.052 0.004 0.012 0.932
#> TCGA-08-0375-01A-01 3 0.6033 0.39574 0.184 0.004 0.616 0.004 0.192
#> TCGA-08-0511-01A-01 3 0.5678 0.44785 0.004 0.060 0.716 0.124 0.096
#> TCGA-08-0514-01A-01 3 0.5789 0.46739 0.004 0.104 0.712 0.080 0.100
#> TCGA-08-0518-01A-01 3 0.4655 0.37915 0.312 0.004 0.660 0.024 0.000
#> TCGA-08-0529-01A-02 3 0.3292 0.49728 0.004 0.056 0.872 0.024 0.044
#> TCGA-08-0531-01A-01 3 0.6185 0.43540 0.004 0.088 0.676 0.092 0.140
#> TCGA-02-0057-01A-01 3 0.6011 0.48486 0.048 0.128 0.708 0.088 0.028
#> TCGA-02-0004-01A-01 2 0.2522 0.77183 0.000 0.880 0.000 0.012 0.108
#> TCGA-02-0006-01B-01 3 0.6861 0.33046 0.004 0.380 0.472 0.108 0.036
#> TCGA-02-0025-01A-01 2 0.4650 0.52750 0.000 0.668 0.008 0.020 0.304
#> TCGA-02-0033-01A-01 2 0.0404 0.83560 0.000 0.988 0.012 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0404 0.83560 0.000 0.988 0.012 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.6595 0.39874 0.000 0.604 0.152 0.052 0.192
#> TCGA-02-0051-01A-01 2 0.3942 0.64204 0.000 0.748 0.000 0.020 0.232
#> TCGA-02-0054-01A-01 3 0.6959 0.34245 0.004 0.364 0.480 0.108 0.044
#> TCGA-02-0055-01A-01 2 0.2921 0.75303 0.000 0.856 0.000 0.020 0.124
#> TCGA-02-0059-01A-01 2 0.4437 0.51858 0.000 0.664 0.000 0.020 0.316
#> TCGA-02-0064-01A-01 3 0.5778 0.37738 0.064 0.304 0.608 0.024 0.000
#> TCGA-02-0075-01A-01 3 0.6020 0.43996 0.160 0.172 0.644 0.024 0.000
#> TCGA-02-0079-01A-03 5 0.2907 0.60943 0.000 0.116 0.012 0.008 0.864
#> TCGA-02-0085-01A-01 4 0.6143 0.48118 0.000 0.128 0.156 0.660 0.056
#> TCGA-02-0086-01A-01 2 0.1430 0.81164 0.000 0.944 0.052 0.000 0.004
#> TCGA-02-0099-01A-01 3 0.6954 0.33416 0.004 0.376 0.468 0.112 0.040
#> TCGA-02-0106-01A-01 2 0.0404 0.83560 0.000 0.988 0.012 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0609 0.83377 0.000 0.980 0.020 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.3690 0.68230 0.000 0.780 0.000 0.020 0.200
#> TCGA-02-0326-01A-01 5 0.2270 0.62781 0.000 0.052 0.020 0.012 0.916
#> TCGA-02-0337-01A-01 2 0.5589 0.20312 0.000 0.548 0.080 0.000 0.372
#> TCGA-06-0122-01A-01 3 0.5407 0.38393 0.304 0.040 0.632 0.024 0.000
#> TCGA-06-0124-01A-01 3 0.5631 0.44916 0.108 0.188 0.680 0.024 0.000
#> TCGA-06-0130-01A-01 2 0.0290 0.83479 0.000 0.992 0.008 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0290 0.82982 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0143-01A-01 3 0.5637 0.36888 0.312 0.052 0.612 0.024 0.000
#> TCGA-06-0147-01A-01 2 0.0404 0.83560 0.000 0.988 0.012 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.7909 -0.11690 0.000 0.376 0.268 0.076 0.280
#> TCGA-06-0152-01A-02 5 0.2659 0.63074 0.000 0.052 0.060 0.000 0.888
#> TCGA-06-0154-01A-02 2 0.0510 0.83495 0.000 0.984 0.016 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0510 0.83495 0.000 0.984 0.016 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.6619 0.46180 0.024 0.184 0.644 0.092 0.056
#> TCGA-06-0176-01A-03 2 0.0404 0.83560 0.000 0.988 0.012 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.7188 0.19896 0.000 0.540 0.160 0.224 0.076
#> TCGA-06-0189-01A-05 2 0.4339 0.55105 0.000 0.684 0.000 0.020 0.296
#> TCGA-06-0190-01A-01 2 0.0404 0.83560 0.000 0.988 0.012 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0451 0.83403 0.000 0.988 0.008 0.000 0.004
#> TCGA-06-0197-01A-02 2 0.3278 0.72586 0.000 0.824 0.000 0.020 0.156
#> TCGA-06-0210-01A-01 2 0.1121 0.81771 0.000 0.956 0.044 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.2561 0.72347 0.000 0.856 0.144 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0510 0.83495 0.000 0.984 0.016 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.5283 0.06683 0.000 0.572 0.384 0.012 0.032
#> TCGA-06-0644-01A-02 2 0.2573 0.77171 0.000 0.880 0.000 0.016 0.104
#> TCGA-06-0645-01A-01 2 0.1668 0.82117 0.000 0.940 0.032 0.000 0.028
#> TCGA-08-0346-01A-01 2 0.3882 0.66475 0.000 0.756 0.020 0.000 0.224
#> TCGA-08-0352-01A-01 3 0.7228 0.35665 0.000 0.124 0.552 0.116 0.208
#> TCGA-08-0360-01A-01 2 0.0510 0.83495 0.000 0.984 0.016 0.000 0.000
#> TCGA-08-0390-01A-01 5 0.4701 0.46796 0.000 0.236 0.000 0.060 0.704
#> TCGA-08-0392-01A-01 5 0.4774 0.09050 0.000 0.424 0.000 0.020 0.556
#> TCGA-08-0509-01A-01 2 0.0510 0.83495 0.000 0.984 0.016 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.4824 0.48314 0.092 0.124 0.760 0.024 0.000
#> TCGA-08-0512-01A-01 2 0.0510 0.83495 0.000 0.984 0.016 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0404 0.83560 0.000 0.988 0.012 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0794 0.82914 0.000 0.972 0.028 0.000 0.000
#> TCGA-12-0620-01A-01 5 0.3099 0.59991 0.000 0.132 0.012 0.008 0.848
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.2257 0.7937 0.900 0.000 0.004 0.008 0.012 0.076
#> TCGA-02-0010-01A-01 1 0.1714 0.7921 0.908 0.000 0.092 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.2084 0.8055 0.916 0.000 0.024 0.016 0.000 0.044
#> TCGA-02-0014-01A-01 1 0.1444 0.8010 0.928 0.000 0.072 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0837 0.8058 0.972 0.000 0.000 0.004 0.004 0.020
#> TCGA-02-0026-01B-01 1 0.1556 0.8000 0.920 0.000 0.080 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.1863 0.7844 0.896 0.000 0.104 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.2122 0.8032 0.900 0.000 0.076 0.000 0.000 0.024
#> TCGA-02-0047-01A-01 6 0.4075 0.6241 0.068 0.004 0.036 0.084 0.004 0.804
#> TCGA-02-0048-01A-01 1 0.4197 0.5021 0.660 0.000 0.008 0.004 0.012 0.316
#> TCGA-02-0060-01A-01 1 0.6105 0.4438 0.560 0.000 0.016 0.220 0.012 0.192
#> TCGA-02-0069-01A-01 1 0.1765 0.7897 0.904 0.000 0.096 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.2048 0.7729 0.880 0.000 0.120 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.6689 0.3761 0.512 0.000 0.044 0.024 0.136 0.284
#> TCGA-02-0084-01A-03 5 0.4823 0.5850 0.004 0.020 0.032 0.020 0.708 0.216
#> TCGA-02-0087-01A-01 5 0.6689 0.2334 0.128 0.000 0.040 0.020 0.444 0.368
#> TCGA-02-0104-01A-01 5 0.6078 0.2873 0.024 0.024 0.048 0.264 0.608 0.032
#> TCGA-02-0114-01A-01 1 0.1444 0.8010 0.928 0.000 0.072 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.1501 0.7999 0.924 0.000 0.076 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.4039 0.5732 0.016 0.004 0.012 0.000 0.720 0.248
#> TCGA-02-0325-01A-01 3 0.5092 0.5225 0.296 0.000 0.628 0.012 0.012 0.052
#> TCGA-02-0338-01A-01 1 0.1501 0.7999 0.924 0.000 0.076 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.1501 0.7999 0.924 0.000 0.076 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.6540 0.3812 0.516 0.000 0.032 0.024 0.136 0.292
#> TCGA-02-0439-01A-01 6 0.3346 0.6110 0.012 0.000 0.028 0.020 0.096 0.844
#> TCGA-02-0440-01A-01 1 0.2350 0.7926 0.896 0.000 0.004 0.008 0.016 0.076
#> TCGA-02-0446-01A-01 6 0.5403 0.4853 0.220 0.004 0.020 0.092 0.008 0.656
#> TCGA-06-0128-01A-01 1 0.3758 0.6654 0.740 0.000 0.232 0.004 0.000 0.024
#> TCGA-06-0129-01A-01 1 0.3081 0.6629 0.776 0.000 0.220 0.000 0.000 0.004
#> TCGA-06-0146-01A-01 1 0.3413 0.7463 0.816 0.000 0.144 0.020 0.004 0.016
#> TCGA-06-0156-01A-01 6 0.4897 0.6149 0.124 0.064 0.028 0.024 0.008 0.752
#> TCGA-06-0166-01A-01 6 0.4382 0.6388 0.068 0.072 0.004 0.024 0.036 0.796
#> TCGA-06-0174-01A-01 1 0.2405 0.7908 0.892 0.000 0.004 0.008 0.016 0.080
#> TCGA-06-0177-01A-01 1 0.5040 0.5704 0.672 0.000 0.016 0.012 0.236 0.064
#> TCGA-06-0238-01A-02 5 0.3662 0.5380 0.000 0.024 0.032 0.088 0.832 0.024
#> TCGA-06-0241-01A-02 1 0.2346 0.7906 0.892 0.000 0.004 0.004 0.016 0.084
#> TCGA-06-0410-01A-01 1 0.6248 0.5528 0.636 0.000 0.040 0.088 0.076 0.160
#> TCGA-06-0413-01A-01 1 0.1501 0.7999 0.924 0.000 0.076 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.2144 0.7950 0.908 0.000 0.004 0.008 0.012 0.068
#> TCGA-06-0646-01A-01 6 0.4155 0.6491 0.084 0.032 0.020 0.004 0.052 0.808
#> TCGA-06-0648-01A-01 5 0.4819 0.5804 0.088 0.004 0.016 0.020 0.744 0.128
#> TCGA-08-0245-01A-01 1 0.2398 0.7884 0.888 0.000 0.004 0.004 0.016 0.088
#> TCGA-08-0344-01A-01 1 0.5242 0.6468 0.696 0.000 0.024 0.020 0.092 0.168
#> TCGA-08-0347-01A-01 6 0.3921 0.6233 0.068 0.000 0.012 0.024 0.084 0.812
#> TCGA-08-0348-01A-01 6 0.5852 0.3766 0.308 0.000 0.020 0.020 0.084 0.568
#> TCGA-08-0350-01A-01 5 0.4610 0.5798 0.020 0.000 0.028 0.024 0.724 0.204
#> TCGA-08-0353-01A-01 1 0.5577 0.1776 0.512 0.000 0.088 0.004 0.012 0.384
#> TCGA-08-0359-01A-01 6 0.6065 0.1026 0.072 0.000 0.012 0.380 0.040 0.496
#> TCGA-08-0385-01A-01 5 0.3092 0.6269 0.004 0.012 0.016 0.020 0.864 0.084
#> TCGA-08-0517-01A-01 1 0.3056 0.7255 0.804 0.000 0.004 0.000 0.008 0.184
#> TCGA-08-0524-01A-01 1 0.1881 0.7996 0.928 0.000 0.004 0.008 0.020 0.040
#> TCGA-12-0616-01A-01 5 0.4488 0.5596 0.080 0.012 0.032 0.020 0.792 0.064
#> TCGA-12-0618-01A-01 1 0.2580 0.7922 0.892 0.000 0.012 0.012 0.020 0.064
#> TCGA-02-0089-01A-01 6 0.4166 0.6163 0.020 0.008 0.052 0.144 0.000 0.776
#> TCGA-02-0113-01A-01 6 0.4229 0.6568 0.024 0.040 0.120 0.020 0.004 0.792
#> TCGA-02-0115-01A-01 4 0.4866 0.0795 0.008 0.000 0.040 0.508 0.000 0.444
#> TCGA-02-0451-01A-01 6 0.4038 0.6413 0.036 0.012 0.048 0.088 0.004 0.812
#> TCGA-06-0132-01A-02 4 0.2274 0.7145 0.008 0.000 0.000 0.892 0.012 0.088
#> TCGA-06-0133-01A-02 4 0.2924 0.6810 0.000 0.000 0.028 0.864 0.024 0.084
#> TCGA-06-0138-01A-02 5 0.6212 0.1925 0.004 0.024 0.048 0.320 0.548 0.056
#> TCGA-06-0160-01A-01 4 0.2013 0.7139 0.008 0.000 0.000 0.908 0.008 0.076
#> TCGA-06-0162-01A-01 5 0.5932 -0.0480 0.000 0.024 0.052 0.448 0.448 0.028
#> TCGA-06-0167-01A-01 4 0.2013 0.7139 0.008 0.000 0.000 0.908 0.008 0.076
#> TCGA-06-0171-01A-02 6 0.7447 -0.2500 0.008 0.024 0.040 0.328 0.244 0.356
#> TCGA-06-0173-01A-01 6 0.4183 0.6506 0.052 0.040 0.080 0.024 0.000 0.804
#> TCGA-06-0179-01A-02 4 0.1858 0.7133 0.012 0.000 0.000 0.924 0.012 0.052
#> TCGA-06-0182-01A-01 5 0.6777 0.1715 0.004 0.024 0.060 0.288 0.520 0.104
#> TCGA-06-0185-01A-01 6 0.5789 0.3985 0.024 0.004 0.036 0.220 0.072 0.644
#> TCGA-06-0195-01B-01 4 0.1757 0.7137 0.012 0.000 0.000 0.928 0.008 0.052
#> TCGA-06-0208-01B-01 6 0.7109 -0.0592 0.032 0.020 0.044 0.368 0.092 0.444
#> TCGA-06-0214-01A-02 6 0.3977 0.6493 0.048 0.040 0.024 0.052 0.008 0.828
#> TCGA-06-0219-01A-01 5 0.5978 -0.0319 0.000 0.024 0.056 0.440 0.452 0.028
#> TCGA-06-0221-01A-01 4 0.5932 -0.0780 0.000 0.024 0.052 0.448 0.448 0.028
#> TCGA-06-0237-01A-02 4 0.7355 0.0756 0.004 0.020 0.040 0.324 0.288 0.324
#> TCGA-06-0240-01A-02 4 0.1442 0.6663 0.000 0.000 0.004 0.944 0.040 0.012
#> TCGA-08-0349-01A-01 6 0.5460 0.2506 0.004 0.008 0.024 0.044 0.356 0.564
#> TCGA-08-0380-01A-01 6 0.4897 0.5554 0.000 0.016 0.028 0.108 0.112 0.736
#> TCGA-08-0386-01A-01 6 0.3372 0.6608 0.056 0.004 0.084 0.016 0.000 0.840
#> TCGA-08-0520-01A-01 5 0.6682 0.0233 0.000 0.020 0.040 0.124 0.416 0.400
#> TCGA-02-0007-01A-01 6 0.3857 0.6525 0.040 0.016 0.152 0.004 0.000 0.788
#> TCGA-02-0009-01A-01 3 0.2605 0.8566 0.108 0.000 0.864 0.000 0.000 0.028
#> TCGA-02-0016-01A-01 6 0.4225 0.6030 0.008 0.000 0.128 0.008 0.088 0.768
#> TCGA-02-0021-01A-01 3 0.3123 0.8312 0.056 0.000 0.832 0.000 0.000 0.112
#> TCGA-02-0023-01B-01 5 0.3625 0.5969 0.004 0.000 0.020 0.004 0.768 0.204
#> TCGA-02-0027-01A-01 3 0.2651 0.8540 0.112 0.000 0.860 0.000 0.000 0.028
#> TCGA-02-0038-01A-01 6 0.4184 0.6513 0.024 0.048 0.144 0.008 0.000 0.776
#> TCGA-02-0043-01A-01 3 0.2573 0.8549 0.112 0.000 0.864 0.000 0.000 0.024
#> TCGA-02-0070-01A-01 6 0.5618 0.2672 0.004 0.028 0.076 0.000 0.328 0.564
#> TCGA-02-0102-01A-01 3 0.2605 0.8566 0.108 0.000 0.864 0.000 0.000 0.028
#> TCGA-02-0260-01A-03 3 0.6583 0.1807 0.052 0.000 0.488 0.004 0.296 0.160
#> TCGA-02-0269-01B-01 5 0.4556 0.5693 0.004 0.000 0.060 0.008 0.700 0.228
#> TCGA-02-0285-01A-01 6 0.5038 0.0386 0.008 0.004 0.044 0.000 0.428 0.516
#> TCGA-02-0289-01A-01 6 0.5530 -0.0191 0.004 0.004 0.084 0.004 0.428 0.476
#> TCGA-02-0290-01A-01 5 0.1950 0.6003 0.000 0.032 0.016 0.028 0.924 0.000
#> TCGA-02-0317-01A-01 5 0.3788 0.6032 0.004 0.000 0.024 0.012 0.772 0.188
#> TCGA-02-0333-01A-02 5 0.4738 0.5575 0.004 0.000 0.072 0.008 0.684 0.232
#> TCGA-02-0422-01A-01 6 0.3275 0.6289 0.008 0.000 0.032 0.000 0.140 0.820
#> TCGA-02-0430-01A-01 3 0.4265 0.5250 0.040 0.000 0.660 0.000 0.000 0.300
#> TCGA-06-0125-01A-01 3 0.2573 0.8549 0.112 0.000 0.864 0.000 0.000 0.024
#> TCGA-06-0126-01A-01 3 0.2573 0.8549 0.112 0.000 0.864 0.000 0.000 0.024
#> TCGA-06-0137-01A-03 3 0.3224 0.8127 0.036 0.000 0.828 0.008 0.000 0.128
#> TCGA-06-0145-01A-04 3 0.3076 0.8290 0.044 0.004 0.840 0.000 0.000 0.112
#> TCGA-06-0148-01A-01 3 0.3880 0.7591 0.008 0.032 0.796 0.000 0.024 0.140
#> TCGA-06-0187-01A-01 6 0.4192 0.6483 0.024 0.044 0.164 0.004 0.000 0.764
#> TCGA-06-0211-01B-01 6 0.3634 0.6603 0.036 0.000 0.076 0.016 0.036 0.836
#> TCGA-06-0402-01A-01 3 0.2527 0.8560 0.108 0.000 0.868 0.000 0.000 0.024
#> TCGA-08-0246-01A-01 6 0.3770 0.6242 0.004 0.024 0.032 0.000 0.140 0.800
#> TCGA-08-0354-01A-01 5 0.3331 0.5709 0.000 0.032 0.068 0.040 0.852 0.008
#> TCGA-08-0355-01A-01 5 0.4705 0.1645 0.004 0.004 0.020 0.004 0.528 0.440
#> TCGA-08-0357-01A-01 6 0.3124 0.6375 0.016 0.000 0.032 0.000 0.108 0.844
#> TCGA-08-0358-01A-01 5 0.1590 0.6118 0.000 0.012 0.008 0.028 0.944 0.008
#> TCGA-08-0375-01A-01 6 0.7150 0.0510 0.108 0.000 0.192 0.000 0.288 0.412
#> TCGA-08-0511-01A-01 6 0.3608 0.6599 0.012 0.004 0.156 0.012 0.012 0.804
#> TCGA-08-0514-01A-01 6 0.3483 0.6578 0.008 0.020 0.160 0.000 0.008 0.804
#> TCGA-08-0518-01A-01 3 0.2647 0.8570 0.088 0.000 0.868 0.000 0.000 0.044
#> TCGA-08-0529-01A-02 6 0.3926 0.6132 0.012 0.012 0.244 0.000 0.004 0.728
#> TCGA-08-0531-01A-01 6 0.3046 0.6667 0.008 0.004 0.112 0.000 0.028 0.848
#> TCGA-02-0057-01A-01 6 0.5163 0.3764 0.000 0.076 0.352 0.008 0.000 0.564
#> TCGA-02-0004-01A-01 2 0.2732 0.8433 0.000 0.880 0.056 0.020 0.044 0.000
#> TCGA-02-0006-01B-01 6 0.5228 0.5641 0.004 0.204 0.116 0.016 0.000 0.660
#> TCGA-02-0025-01A-01 2 0.4197 0.7297 0.000 0.752 0.052 0.020 0.176 0.000
#> TCGA-02-0033-01A-01 2 0.0713 0.9046 0.000 0.972 0.000 0.000 0.000 0.028
#> TCGA-02-0034-01A-01 2 0.0858 0.9039 0.000 0.968 0.004 0.000 0.000 0.028
#> TCGA-02-0039-01A-01 6 0.5980 0.2746 0.000 0.336 0.016 0.000 0.156 0.492
#> TCGA-02-0051-01A-01 2 0.3958 0.7638 0.000 0.784 0.060 0.020 0.136 0.000
#> TCGA-02-0054-01A-01 6 0.5046 0.5880 0.004 0.168 0.124 0.016 0.000 0.688
#> TCGA-02-0055-01A-01 2 0.2732 0.8431 0.000 0.880 0.056 0.020 0.044 0.000
#> TCGA-02-0059-01A-01 2 0.4619 0.6815 0.000 0.716 0.060 0.028 0.196 0.000
#> TCGA-02-0064-01A-01 3 0.3387 0.7418 0.000 0.164 0.796 0.000 0.000 0.040
#> TCGA-02-0075-01A-01 3 0.3173 0.8184 0.024 0.092 0.848 0.000 0.000 0.036
#> TCGA-02-0079-01A-03 5 0.2895 0.6211 0.000 0.044 0.020 0.012 0.880 0.044
#> TCGA-02-0085-01A-01 4 0.5392 0.2439 0.008 0.068 0.004 0.540 0.004 0.376
#> TCGA-02-0086-01A-01 2 0.2278 0.8285 0.000 0.868 0.004 0.000 0.000 0.128
#> TCGA-02-0099-01A-01 6 0.5232 0.5709 0.004 0.188 0.128 0.016 0.000 0.664
#> TCGA-02-0106-01A-01 2 0.0972 0.9042 0.000 0.964 0.000 0.008 0.000 0.028
#> TCGA-02-0107-01A-01 2 0.0777 0.9044 0.000 0.972 0.004 0.000 0.000 0.024
#> TCGA-02-0111-01A-01 2 0.3652 0.7867 0.000 0.808 0.056 0.016 0.120 0.000
#> TCGA-02-0326-01A-01 5 0.2025 0.6262 0.004 0.008 0.008 0.012 0.924 0.044
#> TCGA-02-0337-01A-01 5 0.5915 0.1511 0.004 0.424 0.012 0.000 0.436 0.124
#> TCGA-06-0122-01A-01 3 0.2865 0.8569 0.080 0.020 0.868 0.000 0.000 0.032
#> TCGA-06-0124-01A-01 3 0.3429 0.7978 0.012 0.108 0.824 0.000 0.000 0.056
#> TCGA-06-0130-01A-01 2 0.0632 0.9042 0.000 0.976 0.000 0.000 0.000 0.024
#> TCGA-06-0139-01A-01 2 0.0748 0.8993 0.000 0.976 0.004 0.004 0.000 0.016
#> TCGA-06-0143-01A-01 3 0.2924 0.8541 0.084 0.028 0.864 0.000 0.000 0.024
#> TCGA-06-0147-01A-01 2 0.0777 0.9044 0.000 0.972 0.004 0.000 0.000 0.024
#> TCGA-06-0149-01A-05 6 0.4418 0.6017 0.000 0.100 0.016 0.000 0.140 0.744
#> TCGA-06-0152-01A-02 5 0.2620 0.6261 0.004 0.008 0.012 0.008 0.884 0.084
#> TCGA-06-0154-01A-02 2 0.0935 0.9032 0.000 0.964 0.004 0.000 0.000 0.032
#> TCGA-06-0164-01A-01 2 0.0935 0.9032 0.000 0.964 0.004 0.000 0.000 0.032
#> TCGA-06-0175-01A-01 6 0.4422 0.6542 0.048 0.052 0.120 0.008 0.000 0.772
#> TCGA-06-0176-01A-03 2 0.0858 0.9045 0.000 0.968 0.000 0.004 0.000 0.028
#> TCGA-06-0184-01A-01 6 0.5033 0.2172 0.000 0.416 0.004 0.024 0.024 0.532
#> TCGA-06-0189-01A-05 2 0.4401 0.7177 0.000 0.744 0.060 0.028 0.168 0.000
#> TCGA-06-0190-01A-01 2 0.0713 0.9046 0.000 0.972 0.000 0.000 0.000 0.028
#> TCGA-06-0194-01A-01 2 0.0858 0.9048 0.000 0.968 0.004 0.000 0.000 0.028
#> TCGA-06-0197-01A-02 2 0.3397 0.8112 0.000 0.836 0.056 0.024 0.084 0.000
#> TCGA-06-0210-01A-01 2 0.2320 0.8189 0.000 0.864 0.004 0.000 0.000 0.132
#> TCGA-06-0397-01A-01 2 0.2442 0.8057 0.000 0.852 0.004 0.000 0.000 0.144
#> TCGA-06-0409-01A-02 2 0.0935 0.9032 0.000 0.964 0.004 0.000 0.000 0.032
#> TCGA-06-0412-01A-01 6 0.4886 0.2177 0.004 0.468 0.048 0.000 0.000 0.480
#> TCGA-06-0644-01A-02 2 0.2594 0.8478 0.000 0.888 0.056 0.020 0.036 0.000
#> TCGA-06-0645-01A-01 2 0.1793 0.8892 0.000 0.928 0.004 0.000 0.032 0.036
#> TCGA-08-0346-01A-01 2 0.4766 0.7035 0.000 0.720 0.032 0.012 0.192 0.044
#> TCGA-08-0352-01A-01 6 0.4355 0.6387 0.016 0.032 0.052 0.004 0.108 0.788
#> TCGA-08-0360-01A-01 2 0.0935 0.9032 0.000 0.964 0.004 0.000 0.000 0.032
#> TCGA-08-0390-01A-01 5 0.5324 0.3841 0.000 0.268 0.040 0.048 0.636 0.008
#> TCGA-08-0392-01A-01 5 0.5746 0.1714 0.000 0.368 0.064 0.048 0.520 0.000
#> TCGA-08-0509-01A-01 2 0.1152 0.8971 0.000 0.952 0.004 0.000 0.000 0.044
#> TCGA-08-0510-01A-01 3 0.3347 0.7988 0.004 0.068 0.824 0.000 0.000 0.104
#> TCGA-08-0512-01A-01 2 0.0935 0.9032 0.000 0.964 0.004 0.000 0.000 0.032
#> TCGA-08-0522-01A-01 2 0.0713 0.9046 0.000 0.972 0.000 0.000 0.000 0.028
#> TCGA-12-0619-01A-01 2 0.1471 0.8829 0.000 0.932 0.004 0.000 0.000 0.064
#> TCGA-12-0620-01A-01 5 0.3332 0.6137 0.000 0.060 0.028 0.016 0.856 0.040
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> CV:kmeans 167 5.46e-11 2
#> CV:kmeans 49 NA 3
#> CV:kmeans 118 9.00e-24 4
#> CV:kmeans 85 4.64e-34 5
#> CV:kmeans 138 2.36e-39 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "skmeans"]
# you can also extract it by
# res = res_list["CV:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.917 0.925 0.970 0.5033 0.497 0.497
#> 3 3 0.511 0.557 0.785 0.3235 0.683 0.446
#> 4 4 0.596 0.656 0.799 0.1254 0.804 0.493
#> 5 5 0.806 0.759 0.888 0.0690 0.897 0.623
#> 6 6 0.764 0.636 0.805 0.0362 0.931 0.686
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0048-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0084-01A-03 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0087-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0104-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0321-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0325-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0128-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0166-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0174-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0376 0.9569 0.996 0.004
#> TCGA-06-0238-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.1843 0.9374 0.972 0.028
#> TCGA-06-0413-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0646-01A-01 1 0.0938 0.9506 0.988 0.012
#> TCGA-06-0648-01A-01 2 0.0938 0.9658 0.012 0.988
#> TCGA-08-0245-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.7299 0.7439 0.796 0.204
#> TCGA-08-0347-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0348-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-08-0350-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0353-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.0672 0.9539 0.992 0.008
#> TCGA-08-0385-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-12-0616-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-12-0618-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.9522 0.3973 0.372 0.628
#> TCGA-02-0115-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0451-01A-01 1 0.7602 0.7174 0.780 0.220
#> TCGA-06-0132-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0138-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.7299 0.7438 0.796 0.204
#> TCGA-06-0162-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.7299 0.7438 0.796 0.204
#> TCGA-06-0171-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0173-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0179-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0185-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.5294 0.8473 0.880 0.120
#> TCGA-06-0208-01B-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0221-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0237-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0240-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0349-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-08-0520-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0007-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0009-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0016-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0021-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0023-01B-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0038-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0043-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0070-01A-01 1 0.9944 0.1614 0.544 0.456
#> TCGA-02-0102-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0260-01A-03 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0269-01B-01 2 0.9710 0.2986 0.400 0.600
#> TCGA-02-0285-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0289-01A-01 1 1.0000 0.0505 0.504 0.496
#> TCGA-02-0290-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0317-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0333-01A-02 2 0.9710 0.2986 0.400 0.600
#> TCGA-02-0422-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0430-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0125-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0126-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0137-01A-03 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0145-01A-04 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0148-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0187-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0211-01B-01 1 0.9460 0.4504 0.636 0.364
#> TCGA-06-0402-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-08-0246-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0357-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0358-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0375-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-08-0511-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-08-0514-01A-01 1 0.2948 0.9164 0.948 0.052
#> TCGA-08-0518-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-08-0529-01A-02 1 0.0000 0.9597 1.000 0.000
#> TCGA-08-0531-01A-01 1 0.8327 0.6496 0.736 0.264
#> TCGA-02-0057-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0004-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0006-01B-01 1 0.9732 0.3263 0.596 0.404
#> TCGA-02-0025-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0376 0.9734 0.004 0.996
#> TCGA-02-0039-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0054-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0064-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0075-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-02-0079-01A-03 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0099-01A-01 1 0.0938 0.9508 0.988 0.012
#> TCGA-02-0106-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-02-0337-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0122-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0124-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0143-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0175-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0397-01A-01 1 0.8813 0.5713 0.700 0.300
#> TCGA-06-0409-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.8267 0.6362 0.260 0.740
#> TCGA-06-0644-01A-02 2 0.0000 0.9770 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.1184 0.9623 0.016 0.984
#> TCGA-08-0360-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9770 0.000 1.000
#> TCGA-08-0510-01A-01 1 0.0000 0.9597 1.000 0.000
#> TCGA-08-0512-01A-01 2 0.0672 0.9699 0.008 0.992
#> TCGA-08-0522-01A-01 2 0.0672 0.9699 0.008 0.992
#> TCGA-12-0619-01A-01 2 0.9286 0.4652 0.344 0.656
#> TCGA-12-0620-01A-01 2 0.0000 0.9770 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0237 0.8215 0.996 0.000 0.004
#> TCGA-02-0010-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 1 0.9243 0.2639 0.532 0.232 0.236
#> TCGA-02-0048-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.4555 0.6298 0.800 0.000 0.200
#> TCGA-02-0069-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.4504 0.6314 0.804 0.000 0.196
#> TCGA-02-0084-01A-03 3 0.1753 0.6900 0.000 0.048 0.952
#> TCGA-02-0087-01A-01 1 0.4504 0.6314 0.804 0.000 0.196
#> TCGA-02-0104-01A-01 3 0.5254 0.5844 0.264 0.000 0.736
#> TCGA-02-0114-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.2261 0.6752 0.000 0.068 0.932
#> TCGA-02-0325-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.4842 0.5905 0.776 0.000 0.224
#> TCGA-02-0439-01A-01 3 0.6286 0.2289 0.464 0.000 0.536
#> TCGA-02-0440-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.3649 0.7538 0.896 0.068 0.036
#> TCGA-06-0128-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 1 0.0475 0.8199 0.992 0.004 0.004
#> TCGA-06-0166-01A-01 2 0.7318 0.3817 0.264 0.668 0.068
#> TCGA-06-0174-01A-01 1 0.0237 0.8215 0.996 0.000 0.004
#> TCGA-06-0177-01A-01 1 0.6008 0.2372 0.628 0.000 0.372
#> TCGA-06-0238-01A-02 3 0.0424 0.7080 0.000 0.008 0.992
#> TCGA-06-0241-01A-02 1 0.0237 0.8215 0.996 0.000 0.004
#> TCGA-06-0410-01A-01 1 0.6308 -0.1674 0.508 0.000 0.492
#> TCGA-06-0413-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0237 0.8215 0.996 0.000 0.004
#> TCGA-06-0646-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-06-0648-01A-01 3 0.5656 0.5877 0.264 0.008 0.728
#> TCGA-08-0245-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 3 0.6192 0.3392 0.420 0.000 0.580
#> TCGA-08-0347-01A-01 3 0.5254 0.5844 0.264 0.000 0.736
#> TCGA-08-0348-01A-01 1 0.4504 0.6104 0.804 0.000 0.196
#> TCGA-08-0350-01A-01 3 0.6668 0.5965 0.264 0.040 0.696
#> TCGA-08-0353-01A-01 1 0.1964 0.8067 0.944 0.056 0.000
#> TCGA-08-0359-01A-01 3 0.5650 0.5279 0.312 0.000 0.688
#> TCGA-08-0385-01A-01 3 0.5956 0.5903 0.264 0.016 0.720
#> TCGA-08-0517-01A-01 1 0.0000 0.8231 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0237 0.8215 0.996 0.000 0.004
#> TCGA-12-0616-01A-01 3 0.9340 0.4837 0.264 0.220 0.516
#> TCGA-12-0618-01A-01 1 0.0237 0.8215 0.996 0.000 0.004
#> TCGA-02-0089-01A-01 2 0.6267 -0.1265 0.000 0.548 0.452
#> TCGA-02-0113-01A-01 2 0.5094 0.4615 0.112 0.832 0.056
#> TCGA-02-0115-01A-01 2 0.9242 0.0696 0.228 0.532 0.240
#> TCGA-02-0451-01A-01 2 0.8749 0.1568 0.152 0.572 0.276
#> TCGA-06-0132-01A-02 3 0.0424 0.7066 0.000 0.008 0.992
#> TCGA-06-0133-01A-02 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 3 0.5650 0.5279 0.312 0.000 0.688
#> TCGA-06-0162-01A-01 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 3 0.5650 0.5279 0.312 0.000 0.688
#> TCGA-06-0171-01A-02 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 2 0.7464 -0.1321 0.400 0.560 0.040
#> TCGA-06-0179-01A-02 3 0.0424 0.7066 0.000 0.008 0.992
#> TCGA-06-0182-01A-01 3 0.4452 0.5190 0.000 0.192 0.808
#> TCGA-06-0185-01A-01 3 0.4842 0.5747 0.000 0.224 0.776
#> TCGA-06-0195-01B-01 3 0.5650 0.5279 0.312 0.000 0.688
#> TCGA-06-0208-01B-01 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.5882 0.5719 0.000 0.652 0.348
#> TCGA-06-0219-01A-01 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-08-0349-01A-01 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.8666 0.6015 0.584 0.264 0.152
#> TCGA-08-0520-01A-01 3 0.0000 0.7097 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-02-0009-01A-01 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-02-0016-01A-01 1 0.9099 0.5536 0.544 0.264 0.192
#> TCGA-02-0021-01A-01 1 0.5327 0.7063 0.728 0.272 0.000
#> TCGA-02-0023-01B-01 3 0.0592 0.7067 0.000 0.012 0.988
#> TCGA-02-0027-01A-01 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-02-0038-01A-01 2 0.6771 -0.1965 0.440 0.548 0.012
#> TCGA-02-0043-01A-01 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-02-0070-01A-01 2 0.6988 0.1007 0.320 0.644 0.036
#> TCGA-02-0102-01A-01 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-02-0260-01A-03 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-02-0269-01B-01 3 0.6512 0.5269 0.024 0.300 0.676
#> TCGA-02-0285-01A-01 3 0.6302 0.2981 0.000 0.480 0.520
#> TCGA-02-0289-01A-01 3 0.7889 0.4767 0.088 0.288 0.624
#> TCGA-02-0290-01A-01 3 0.4931 0.4779 0.000 0.232 0.768
#> TCGA-02-0317-01A-01 3 0.1860 0.6975 0.000 0.052 0.948
#> TCGA-02-0333-01A-02 3 0.6512 0.5269 0.024 0.300 0.676
#> TCGA-02-0422-01A-01 3 0.6295 0.3818 0.000 0.472 0.528
#> TCGA-02-0430-01A-01 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-06-0125-01A-01 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-06-0126-01A-01 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-06-0137-01A-03 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-06-0145-01A-04 1 0.5591 0.6733 0.696 0.304 0.000
#> TCGA-06-0148-01A-01 1 0.6252 0.4820 0.556 0.444 0.000
#> TCGA-06-0187-01A-01 2 0.6280 -0.2314 0.460 0.540 0.000
#> TCGA-06-0211-01B-01 3 0.7146 0.5034 0.060 0.264 0.676
#> TCGA-06-0402-01A-01 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-08-0246-01A-01 2 0.6062 0.4866 0.000 0.616 0.384
#> TCGA-08-0354-01A-01 3 0.4931 0.4779 0.000 0.232 0.768
#> TCGA-08-0355-01A-01 3 0.1289 0.6989 0.000 0.032 0.968
#> TCGA-08-0357-01A-01 3 0.5254 0.5396 0.000 0.264 0.736
#> TCGA-08-0358-01A-01 3 0.1411 0.6967 0.000 0.036 0.964
#> TCGA-08-0375-01A-01 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-08-0511-01A-01 2 0.9547 -0.0892 0.292 0.480 0.228
#> TCGA-08-0514-01A-01 2 0.4172 0.4484 0.156 0.840 0.004
#> TCGA-08-0518-01A-01 1 0.5254 0.7134 0.736 0.264 0.000
#> TCGA-08-0529-01A-02 1 0.5678 0.6594 0.684 0.316 0.000
#> TCGA-08-0531-01A-01 3 0.9512 0.1799 0.188 0.384 0.428
#> TCGA-02-0057-01A-01 2 0.6295 -0.2595 0.472 0.528 0.000
#> TCGA-02-0004-01A-01 2 0.5497 0.6108 0.000 0.708 0.292
#> TCGA-02-0006-01B-01 2 0.2173 0.5217 0.048 0.944 0.008
#> TCGA-02-0025-01A-01 3 0.6305 -0.1655 0.000 0.484 0.516
#> TCGA-02-0033-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-02-0034-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-02-0039-01A-01 2 0.6168 0.4652 0.000 0.588 0.412
#> TCGA-02-0051-01A-01 2 0.6280 0.2996 0.000 0.540 0.460
#> TCGA-02-0054-01A-01 2 0.2356 0.5099 0.072 0.928 0.000
#> TCGA-02-0055-01A-01 2 0.5497 0.6108 0.000 0.708 0.292
#> TCGA-02-0059-01A-01 3 0.6299 -0.1407 0.000 0.476 0.524
#> TCGA-02-0064-01A-01 2 0.4842 0.3466 0.224 0.776 0.000
#> TCGA-02-0075-01A-01 2 0.6299 -0.2701 0.476 0.524 0.000
#> TCGA-02-0079-01A-03 3 0.2625 0.6628 0.000 0.084 0.916
#> TCGA-02-0085-01A-01 3 0.6280 -0.2387 0.000 0.460 0.540
#> TCGA-02-0086-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-02-0099-01A-01 2 0.1765 0.5184 0.040 0.956 0.004
#> TCGA-02-0106-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-02-0107-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-02-0111-01A-01 2 0.5678 0.5827 0.000 0.684 0.316
#> TCGA-02-0326-01A-01 3 0.1411 0.6967 0.000 0.036 0.964
#> TCGA-02-0337-01A-01 2 0.5678 0.5841 0.000 0.684 0.316
#> TCGA-06-0122-01A-01 1 0.5591 0.6733 0.696 0.304 0.000
#> TCGA-06-0124-01A-01 2 0.6252 -0.1928 0.444 0.556 0.000
#> TCGA-06-0130-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-06-0139-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-06-0143-01A-01 1 0.5529 0.6824 0.704 0.296 0.000
#> TCGA-06-0147-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-06-0149-01A-05 2 0.5363 0.6239 0.000 0.724 0.276
#> TCGA-06-0152-01A-02 3 0.4291 0.5538 0.000 0.180 0.820
#> TCGA-06-0154-01A-02 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-06-0164-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-06-0175-01A-01 2 0.6291 -0.2494 0.468 0.532 0.000
#> TCGA-06-0176-01A-03 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-06-0184-01A-01 2 0.5926 0.5564 0.000 0.644 0.356
#> TCGA-06-0189-01A-05 3 0.6299 -0.1407 0.000 0.476 0.524
#> TCGA-06-0190-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-06-0194-01A-01 2 0.5397 0.6208 0.000 0.720 0.280
#> TCGA-06-0197-01A-02 2 0.5529 0.6066 0.000 0.704 0.296
#> TCGA-06-0210-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-06-0397-01A-01 2 0.3816 0.4638 0.148 0.852 0.000
#> TCGA-06-0409-01A-02 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-06-0412-01A-01 2 0.0000 0.5259 0.000 1.000 0.000
#> TCGA-06-0644-01A-02 2 0.5497 0.6108 0.000 0.708 0.292
#> TCGA-06-0645-01A-01 2 0.5497 0.6108 0.000 0.708 0.292
#> TCGA-08-0346-01A-01 2 0.5621 0.5926 0.000 0.692 0.308
#> TCGA-08-0352-01A-01 2 0.4654 0.3360 0.000 0.792 0.208
#> TCGA-08-0360-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-08-0390-01A-01 3 0.1163 0.7006 0.000 0.028 0.972
#> TCGA-08-0392-01A-01 3 0.5560 0.3530 0.000 0.300 0.700
#> TCGA-08-0509-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-08-0510-01A-01 2 0.6295 -0.2595 0.472 0.528 0.000
#> TCGA-08-0512-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-08-0522-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-12-0619-01A-01 2 0.5254 0.6324 0.000 0.736 0.264
#> TCGA-12-0620-01A-01 3 0.5397 0.3931 0.000 0.280 0.720
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.0336 0.9073 0.992 0.000 0.008 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0336 0.9073 0.992 0.000 0.008 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 3 0.7883 -0.0928 0.288 0.000 0.376 0.336
#> TCGA-02-0048-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.4356 0.7314 0.804 0.000 0.148 0.048
#> TCGA-02-0069-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.4586 0.7407 0.796 0.000 0.136 0.068
#> TCGA-02-0084-01A-03 4 0.6477 0.4304 0.000 0.300 0.100 0.600
#> TCGA-02-0087-01A-01 1 0.4458 0.7495 0.808 0.000 0.116 0.076
#> TCGA-02-0104-01A-01 4 0.4212 0.6043 0.216 0.000 0.012 0.772
#> TCGA-02-0114-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 4 0.5907 0.5369 0.000 0.228 0.092 0.680
#> TCGA-02-0325-01A-01 1 0.2011 0.8269 0.920 0.000 0.080 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.5091 0.6934 0.752 0.000 0.180 0.068
#> TCGA-02-0439-01A-01 4 0.7536 0.4604 0.228 0.000 0.284 0.488
#> TCGA-02-0440-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.6098 0.5553 0.676 0.000 0.200 0.124
#> TCGA-06-0128-01A-01 1 0.0188 0.9086 0.996 0.000 0.004 0.000
#> TCGA-06-0129-01A-01 1 0.0188 0.9086 0.996 0.000 0.004 0.000
#> TCGA-06-0146-01A-01 1 0.0188 0.9086 0.996 0.000 0.004 0.000
#> TCGA-06-0156-01A-01 1 0.2510 0.8455 0.916 0.064 0.012 0.008
#> TCGA-06-0166-01A-01 2 0.7729 0.3665 0.280 0.552 0.036 0.132
#> TCGA-06-0174-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.2300 0.8514 0.920 0.000 0.016 0.064
#> TCGA-06-0238-01A-02 4 0.1624 0.6977 0.000 0.028 0.020 0.952
#> TCGA-06-0241-01A-02 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.4391 0.6406 0.740 0.000 0.008 0.252
#> TCGA-06-0413-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0188 0.9095 0.996 0.000 0.004 0.000
#> TCGA-06-0646-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-06-0648-01A-01 4 0.5938 0.5619 0.232 0.000 0.092 0.676
#> TCGA-08-0245-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.6248 0.5150 0.656 0.000 0.120 0.224
#> TCGA-08-0347-01A-01 4 0.6184 0.5769 0.120 0.000 0.216 0.664
#> TCGA-08-0348-01A-01 1 0.1510 0.8803 0.956 0.000 0.016 0.028
#> TCGA-08-0350-01A-01 1 0.7010 -0.1420 0.448 0.004 0.100 0.448
#> TCGA-08-0353-01A-01 1 0.2921 0.7219 0.860 0.000 0.140 0.000
#> TCGA-08-0359-01A-01 4 0.7309 0.3875 0.272 0.000 0.200 0.528
#> TCGA-08-0385-01A-01 4 0.6050 0.5583 0.232 0.000 0.100 0.668
#> TCGA-08-0517-01A-01 1 0.0000 0.9111 1.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0188 0.9095 0.996 0.000 0.004 0.000
#> TCGA-12-0616-01A-01 4 0.6776 0.4636 0.304 0.044 0.044 0.608
#> TCGA-12-0618-01A-01 1 0.0188 0.9095 0.996 0.000 0.004 0.000
#> TCGA-02-0089-01A-01 3 0.5503 -0.0956 0.000 0.016 0.516 0.468
#> TCGA-02-0113-01A-01 3 0.7082 0.4510 0.016 0.124 0.600 0.260
#> TCGA-02-0115-01A-01 3 0.4817 0.1533 0.000 0.000 0.612 0.388
#> TCGA-02-0451-01A-01 3 0.5352 0.1353 0.000 0.016 0.596 0.388
#> TCGA-06-0132-01A-02 4 0.3791 0.6271 0.000 0.004 0.200 0.796
#> TCGA-06-0133-01A-02 4 0.3610 0.6272 0.000 0.000 0.200 0.800
#> TCGA-06-0138-01A-02 4 0.0000 0.6983 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 4 0.6497 0.5197 0.160 0.000 0.200 0.640
#> TCGA-06-0162-01A-01 4 0.0000 0.6983 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 4 0.6497 0.5197 0.160 0.000 0.200 0.640
#> TCGA-06-0171-01A-02 4 0.1637 0.6887 0.000 0.000 0.060 0.940
#> TCGA-06-0173-01A-01 3 0.6754 0.2225 0.092 0.008 0.584 0.316
#> TCGA-06-0179-01A-02 4 0.3791 0.6257 0.004 0.000 0.200 0.796
#> TCGA-06-0182-01A-01 4 0.2053 0.6879 0.000 0.072 0.004 0.924
#> TCGA-06-0185-01A-01 4 0.2814 0.6622 0.000 0.000 0.132 0.868
#> TCGA-06-0195-01B-01 4 0.6286 0.5332 0.140 0.000 0.200 0.660
#> TCGA-06-0208-01B-01 4 0.3123 0.6518 0.000 0.000 0.156 0.844
#> TCGA-06-0214-01A-02 2 0.7442 0.0519 0.000 0.456 0.176 0.368
#> TCGA-06-0219-01A-01 4 0.0000 0.6983 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 4 0.0000 0.6983 0.000 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 4 0.0592 0.6963 0.000 0.000 0.016 0.984
#> TCGA-06-0240-01A-02 4 0.3400 0.6397 0.000 0.000 0.180 0.820
#> TCGA-08-0349-01A-01 4 0.1637 0.6885 0.000 0.000 0.060 0.940
#> TCGA-08-0380-01A-01 4 0.2216 0.6802 0.000 0.000 0.092 0.908
#> TCGA-08-0386-01A-01 3 0.4285 0.5641 0.076 0.000 0.820 0.104
#> TCGA-08-0520-01A-01 4 0.0336 0.6983 0.000 0.000 0.008 0.992
#> TCGA-02-0007-01A-01 3 0.4406 0.6902 0.300 0.000 0.700 0.000
#> TCGA-02-0009-01A-01 3 0.4406 0.6902 0.300 0.000 0.700 0.000
#> TCGA-02-0016-01A-01 3 0.3257 0.6988 0.152 0.000 0.844 0.004
#> TCGA-02-0021-01A-01 3 0.4406 0.6902 0.300 0.000 0.700 0.000
#> TCGA-02-0023-01B-01 4 0.3143 0.6804 0.000 0.024 0.100 0.876
#> TCGA-02-0027-01A-01 3 0.4454 0.6829 0.308 0.000 0.692 0.000
#> TCGA-02-0038-01A-01 3 0.4979 0.6797 0.064 0.120 0.796 0.020
#> TCGA-02-0043-01A-01 3 0.4406 0.6902 0.300 0.000 0.700 0.000
#> TCGA-02-0070-01A-01 3 0.7320 0.3084 0.100 0.356 0.524 0.020
#> TCGA-02-0102-01A-01 3 0.4406 0.6902 0.300 0.000 0.700 0.000
#> TCGA-02-0260-01A-03 3 0.4877 0.4256 0.408 0.000 0.592 0.000
#> TCGA-02-0269-01B-01 4 0.4830 0.3859 0.000 0.000 0.392 0.608
#> TCGA-02-0285-01A-01 4 0.7816 0.2389 0.000 0.260 0.340 0.400
#> TCGA-02-0289-01A-01 3 0.3764 0.4985 0.000 0.000 0.784 0.216
#> TCGA-02-0290-01A-01 4 0.6323 0.4707 0.000 0.272 0.100 0.628
#> TCGA-02-0317-01A-01 4 0.6116 0.5707 0.000 0.112 0.220 0.668
#> TCGA-02-0333-01A-02 3 0.5000 -0.1779 0.000 0.000 0.500 0.500
#> TCGA-02-0422-01A-01 3 0.7253 -0.2341 0.000 0.144 0.432 0.424
#> TCGA-02-0430-01A-01 3 0.4406 0.6902 0.300 0.000 0.700 0.000
#> TCGA-06-0125-01A-01 3 0.4406 0.6902 0.300 0.000 0.700 0.000
#> TCGA-06-0126-01A-01 3 0.4406 0.6902 0.300 0.000 0.700 0.000
#> TCGA-06-0137-01A-03 3 0.3444 0.7122 0.184 0.000 0.816 0.000
#> TCGA-06-0145-01A-04 3 0.4927 0.7062 0.264 0.024 0.712 0.000
#> TCGA-06-0148-01A-01 3 0.4669 0.6928 0.104 0.100 0.796 0.000
#> TCGA-06-0187-01A-01 3 0.5209 0.7185 0.140 0.104 0.756 0.000
#> TCGA-06-0211-01B-01 4 0.5151 0.2224 0.004 0.000 0.464 0.532
#> TCGA-06-0402-01A-01 3 0.4406 0.6902 0.300 0.000 0.700 0.000
#> TCGA-08-0246-01A-01 2 0.6403 0.4798 0.000 0.628 0.112 0.260
#> TCGA-08-0354-01A-01 4 0.6347 0.4640 0.000 0.276 0.100 0.624
#> TCGA-08-0355-01A-01 4 0.4083 0.6725 0.000 0.068 0.100 0.832
#> TCGA-08-0357-01A-01 4 0.4998 0.2731 0.000 0.000 0.488 0.512
#> TCGA-08-0358-01A-01 4 0.5923 0.5464 0.000 0.216 0.100 0.684
#> TCGA-08-0375-01A-01 3 0.4999 0.3416 0.492 0.000 0.508 0.000
#> TCGA-08-0511-01A-01 3 0.1792 0.5893 0.000 0.000 0.932 0.068
#> TCGA-08-0514-01A-01 3 0.3703 0.6397 0.008 0.140 0.840 0.012
#> TCGA-08-0518-01A-01 3 0.4406 0.6902 0.300 0.000 0.700 0.000
#> TCGA-08-0529-01A-02 3 0.4399 0.7202 0.212 0.020 0.768 0.000
#> TCGA-08-0531-01A-01 3 0.2973 0.5628 0.000 0.000 0.856 0.144
#> TCGA-02-0057-01A-01 3 0.4775 0.7194 0.140 0.076 0.784 0.000
#> TCGA-02-0004-01A-01 2 0.1118 0.8474 0.000 0.964 0.000 0.036
#> TCGA-02-0006-01B-01 2 0.5742 0.2510 0.000 0.596 0.368 0.036
#> TCGA-02-0025-01A-01 2 0.3166 0.7930 0.000 0.868 0.016 0.116
#> TCGA-02-0033-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.4817 0.7235 0.000 0.784 0.088 0.128
#> TCGA-02-0051-01A-01 2 0.2197 0.8246 0.000 0.916 0.004 0.080
#> TCGA-02-0054-01A-01 3 0.5217 0.4067 0.000 0.380 0.608 0.012
#> TCGA-02-0055-01A-01 2 0.0921 0.8502 0.000 0.972 0.000 0.028
#> TCGA-02-0059-01A-01 2 0.3443 0.7775 0.000 0.848 0.016 0.136
#> TCGA-02-0064-01A-01 3 0.5300 0.5611 0.028 0.308 0.664 0.000
#> TCGA-02-0075-01A-01 3 0.5932 0.7126 0.172 0.132 0.696 0.000
#> TCGA-02-0079-01A-03 4 0.6811 0.1692 0.000 0.404 0.100 0.496
#> TCGA-02-0085-01A-01 4 0.7602 0.1335 0.000 0.380 0.200 0.420
#> TCGA-02-0086-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-02-0099-01A-01 3 0.5417 0.3497 0.000 0.412 0.572 0.016
#> TCGA-02-0106-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.2805 0.8065 0.000 0.888 0.012 0.100
#> TCGA-02-0326-01A-01 4 0.5923 0.5464 0.000 0.216 0.100 0.684
#> TCGA-02-0337-01A-01 2 0.4773 0.7262 0.000 0.788 0.092 0.120
#> TCGA-06-0122-01A-01 3 0.5010 0.7007 0.276 0.024 0.700 0.000
#> TCGA-06-0124-01A-01 3 0.5948 0.7105 0.160 0.144 0.696 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.5169 0.7020 0.272 0.032 0.696 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.3617 0.7920 0.000 0.860 0.076 0.064
#> TCGA-06-0152-01A-02 4 0.6139 0.5119 0.000 0.244 0.100 0.656
#> TCGA-06-0154-01A-02 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.5011 0.7185 0.160 0.076 0.764 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.5626 0.3556 0.000 0.588 0.028 0.384
#> TCGA-06-0189-01A-05 2 0.3142 0.7874 0.000 0.860 0.008 0.132
#> TCGA-06-0190-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.1118 0.8474 0.000 0.964 0.000 0.036
#> TCGA-06-0210-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.2983 0.7820 0.040 0.892 0.068 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.2216 0.7901 0.000 0.908 0.092 0.000
#> TCGA-06-0644-01A-02 2 0.1022 0.8489 0.000 0.968 0.000 0.032
#> TCGA-06-0645-01A-01 2 0.2473 0.8198 0.000 0.908 0.012 0.080
#> TCGA-08-0346-01A-01 2 0.4655 0.7347 0.000 0.796 0.088 0.116
#> TCGA-08-0352-01A-01 2 0.6080 0.3189 0.000 0.488 0.468 0.044
#> TCGA-08-0360-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 4 0.5149 0.4002 0.000 0.336 0.016 0.648
#> TCGA-08-0392-01A-01 2 0.5298 0.3824 0.000 0.612 0.016 0.372
#> TCGA-08-0509-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.5594 0.7191 0.164 0.112 0.724 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.8575 0.000 1.000 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.6766 0.1979 0.000 0.520 0.100 0.380
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.0162 0.9418 0.996 0.000 0.000 0.004 0.000
#> TCGA-02-0010-01A-01 1 0.0162 0.9421 0.996 0.000 0.004 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0404 0.9396 0.988 0.000 0.012 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0162 0.9421 0.996 0.000 0.004 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0794 0.9320 0.972 0.000 0.028 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0162 0.9421 0.996 0.000 0.004 0.000 0.000
#> TCGA-02-0047-01A-01 4 0.0912 0.7641 0.012 0.000 0.016 0.972 0.000
#> TCGA-02-0048-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.2966 0.7896 0.816 0.000 0.000 0.184 0.000
#> TCGA-02-0069-01A-01 1 0.0404 0.9396 0.988 0.000 0.012 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0609 0.9361 0.980 0.000 0.020 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.4788 0.7411 0.760 0.000 0.068 0.028 0.144
#> TCGA-02-0084-01A-03 5 0.0981 0.8124 0.000 0.012 0.008 0.008 0.972
#> TCGA-02-0087-01A-01 5 0.5343 0.0114 0.468 0.000 0.024 0.016 0.492
#> TCGA-02-0104-01A-01 5 0.5892 0.3190 0.220 0.000 0.000 0.180 0.600
#> TCGA-02-0114-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.0162 0.8128 0.000 0.000 0.000 0.004 0.996
#> TCGA-02-0325-01A-01 1 0.3521 0.7089 0.764 0.000 0.232 0.000 0.004
#> TCGA-02-0338-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.4432 0.7505 0.772 0.000 0.008 0.076 0.144
#> TCGA-02-0439-01A-01 4 0.5084 -0.0218 0.020 0.000 0.008 0.488 0.484
#> TCGA-02-0440-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.4219 0.3627 0.584 0.000 0.000 0.416 0.000
#> TCGA-06-0128-01A-01 1 0.1270 0.9176 0.948 0.000 0.052 0.000 0.000
#> TCGA-06-0129-01A-01 1 0.1270 0.9176 0.948 0.000 0.052 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.1043 0.9250 0.960 0.000 0.040 0.000 0.000
#> TCGA-06-0156-01A-01 1 0.1557 0.9097 0.940 0.008 0.000 0.052 0.000
#> TCGA-06-0166-01A-01 2 0.6768 0.3361 0.248 0.524 0.000 0.208 0.020
#> TCGA-06-0174-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0162 0.9416 0.996 0.000 0.000 0.000 0.004
#> TCGA-06-0238-01A-02 5 0.2127 0.7043 0.000 0.000 0.000 0.108 0.892
#> TCGA-06-0241-01A-02 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.1965 0.8946 0.924 0.000 0.000 0.052 0.024
#> TCGA-06-0413-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 1 0.2646 0.8324 0.868 0.000 0.004 0.004 0.124
#> TCGA-06-0648-01A-01 5 0.1124 0.7964 0.036 0.000 0.000 0.004 0.960
#> TCGA-08-0245-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.3224 0.7955 0.824 0.000 0.000 0.160 0.016
#> TCGA-08-0347-01A-01 4 0.4622 0.1303 0.012 0.000 0.000 0.548 0.440
#> TCGA-08-0348-01A-01 1 0.0404 0.9379 0.988 0.000 0.000 0.000 0.012
#> TCGA-08-0350-01A-01 5 0.0671 0.8117 0.016 0.000 0.004 0.000 0.980
#> TCGA-08-0353-01A-01 1 0.2377 0.8449 0.872 0.000 0.128 0.000 0.000
#> TCGA-08-0359-01A-01 4 0.2969 0.6763 0.128 0.000 0.000 0.852 0.020
#> TCGA-08-0385-01A-01 5 0.0000 0.8138 0.000 0.000 0.000 0.000 1.000
#> TCGA-08-0517-01A-01 1 0.0162 0.9416 0.996 0.000 0.004 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 5 0.2891 0.6572 0.176 0.000 0.000 0.000 0.824
#> TCGA-12-0618-01A-01 1 0.0000 0.9428 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 4 0.0000 0.7709 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0113-01A-01 4 0.4748 -0.0451 0.000 0.016 0.492 0.492 0.000
#> TCGA-02-0115-01A-01 4 0.0404 0.7682 0.000 0.000 0.012 0.988 0.000
#> TCGA-02-0451-01A-01 4 0.0290 0.7694 0.000 0.000 0.008 0.992 0.000
#> TCGA-06-0132-01A-02 4 0.0162 0.7719 0.000 0.000 0.000 0.996 0.004
#> TCGA-06-0133-01A-02 4 0.0162 0.7719 0.000 0.000 0.000 0.996 0.004
#> TCGA-06-0138-01A-02 4 0.4210 0.4889 0.000 0.000 0.000 0.588 0.412
#> TCGA-06-0160-01A-01 4 0.0162 0.7719 0.000 0.000 0.000 0.996 0.004
#> TCGA-06-0162-01A-01 4 0.4210 0.4889 0.000 0.000 0.000 0.588 0.412
#> TCGA-06-0167-01A-01 4 0.0162 0.7719 0.000 0.000 0.000 0.996 0.004
#> TCGA-06-0171-01A-02 4 0.3109 0.7024 0.000 0.000 0.000 0.800 0.200
#> TCGA-06-0173-01A-01 4 0.1739 0.7551 0.032 0.004 0.024 0.940 0.000
#> TCGA-06-0179-01A-02 4 0.0162 0.7719 0.000 0.000 0.000 0.996 0.004
#> TCGA-06-0182-01A-01 4 0.4767 0.4587 0.000 0.020 0.000 0.560 0.420
#> TCGA-06-0185-01A-01 4 0.3086 0.7146 0.000 0.000 0.004 0.816 0.180
#> TCGA-06-0195-01B-01 4 0.0162 0.7719 0.000 0.000 0.000 0.996 0.004
#> TCGA-06-0208-01B-01 4 0.1908 0.7543 0.000 0.000 0.000 0.908 0.092
#> TCGA-06-0214-01A-02 4 0.0807 0.7696 0.000 0.012 0.000 0.976 0.012
#> TCGA-06-0219-01A-01 4 0.4210 0.4889 0.000 0.000 0.000 0.588 0.412
#> TCGA-06-0221-01A-01 4 0.4210 0.4889 0.000 0.000 0.000 0.588 0.412
#> TCGA-06-0237-01A-02 4 0.3999 0.5755 0.000 0.000 0.000 0.656 0.344
#> TCGA-06-0240-01A-02 4 0.0162 0.7719 0.000 0.000 0.000 0.996 0.004
#> TCGA-08-0349-01A-01 4 0.3895 0.5988 0.000 0.000 0.000 0.680 0.320
#> TCGA-08-0380-01A-01 4 0.2286 0.7478 0.000 0.004 0.000 0.888 0.108
#> TCGA-08-0386-01A-01 3 0.5542 0.2820 0.072 0.000 0.532 0.396 0.000
#> TCGA-08-0520-01A-01 4 0.4249 0.4551 0.000 0.000 0.000 0.568 0.432
#> TCGA-02-0007-01A-01 3 0.0771 0.8930 0.020 0.000 0.976 0.004 0.000
#> TCGA-02-0009-01A-01 3 0.0404 0.8949 0.012 0.000 0.988 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.2339 0.8527 0.008 0.000 0.912 0.028 0.052
#> TCGA-02-0021-01A-01 3 0.0290 0.8945 0.008 0.000 0.992 0.000 0.000
#> TCGA-02-0023-01B-01 5 0.0324 0.8132 0.000 0.000 0.004 0.004 0.992
#> TCGA-02-0027-01A-01 3 0.0609 0.8938 0.020 0.000 0.980 0.000 0.000
#> TCGA-02-0038-01A-01 3 0.1205 0.8787 0.000 0.004 0.956 0.040 0.000
#> TCGA-02-0043-01A-01 3 0.0609 0.8938 0.020 0.000 0.980 0.000 0.000
#> TCGA-02-0070-01A-01 5 0.4969 0.0485 0.004 0.020 0.468 0.000 0.508
#> TCGA-02-0102-01A-01 3 0.0510 0.8945 0.016 0.000 0.984 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.4851 0.3891 0.036 0.000 0.624 0.000 0.340
#> TCGA-02-0269-01B-01 5 0.0880 0.8083 0.000 0.000 0.032 0.000 0.968
#> TCGA-02-0285-01A-01 5 0.0703 0.8116 0.000 0.000 0.024 0.000 0.976
#> TCGA-02-0289-01A-01 5 0.3816 0.5284 0.000 0.000 0.304 0.000 0.696
#> TCGA-02-0290-01A-01 5 0.0000 0.8138 0.000 0.000 0.000 0.000 1.000
#> TCGA-02-0317-01A-01 5 0.0404 0.8135 0.000 0.000 0.012 0.000 0.988
#> TCGA-02-0333-01A-02 5 0.2179 0.7558 0.000 0.000 0.112 0.000 0.888
#> TCGA-02-0422-01A-01 5 0.2536 0.7400 0.000 0.000 0.128 0.004 0.868
#> TCGA-02-0430-01A-01 3 0.0404 0.8948 0.012 0.000 0.988 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0609 0.8938 0.020 0.000 0.980 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.0609 0.8938 0.020 0.000 0.980 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.0671 0.8919 0.004 0.000 0.980 0.016 0.000
#> TCGA-06-0145-01A-04 3 0.0162 0.8939 0.004 0.000 0.996 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.8927 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0187-01A-01 3 0.0324 0.8928 0.000 0.004 0.992 0.004 0.000
#> TCGA-06-0211-01B-01 4 0.5555 0.5844 0.000 0.000 0.204 0.644 0.152
#> TCGA-06-0402-01A-01 3 0.0609 0.8938 0.020 0.000 0.980 0.000 0.000
#> TCGA-08-0246-01A-01 5 0.4570 0.4203 0.000 0.332 0.016 0.004 0.648
#> TCGA-08-0354-01A-01 5 0.0324 0.8123 0.000 0.004 0.000 0.004 0.992
#> TCGA-08-0355-01A-01 5 0.0404 0.8135 0.000 0.000 0.012 0.000 0.988
#> TCGA-08-0357-01A-01 5 0.3921 0.6925 0.000 0.000 0.128 0.072 0.800
#> TCGA-08-0358-01A-01 5 0.0000 0.8138 0.000 0.000 0.000 0.000 1.000
#> TCGA-08-0375-01A-01 3 0.5026 0.4898 0.064 0.000 0.656 0.000 0.280
#> TCGA-08-0511-01A-01 3 0.3878 0.6644 0.000 0.000 0.748 0.236 0.016
#> TCGA-08-0514-01A-01 3 0.1282 0.8686 0.000 0.000 0.952 0.004 0.044
#> TCGA-08-0518-01A-01 3 0.0404 0.8949 0.012 0.000 0.988 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.8927 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.2806 0.7606 0.000 0.000 0.844 0.004 0.152
#> TCGA-02-0057-01A-01 3 0.2069 0.8509 0.000 0.012 0.912 0.076 0.000
#> TCGA-02-0004-01A-01 2 0.0404 0.8971 0.000 0.988 0.000 0.000 0.012
#> TCGA-02-0006-01B-01 2 0.4953 0.5808 0.000 0.696 0.216 0.088 0.000
#> TCGA-02-0025-01A-01 2 0.2377 0.8165 0.000 0.872 0.000 0.000 0.128
#> TCGA-02-0033-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.3990 0.5692 0.000 0.688 0.000 0.004 0.308
#> TCGA-02-0051-01A-01 2 0.0703 0.8927 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0054-01A-01 3 0.5713 0.2093 0.000 0.416 0.500 0.084 0.000
#> TCGA-02-0055-01A-01 2 0.0404 0.8971 0.000 0.988 0.000 0.000 0.012
#> TCGA-02-0059-01A-01 2 0.2074 0.8385 0.000 0.896 0.000 0.000 0.104
#> TCGA-02-0064-01A-01 3 0.1544 0.8589 0.000 0.068 0.932 0.000 0.000
#> TCGA-02-0075-01A-01 3 0.0703 0.8889 0.000 0.024 0.976 0.000 0.000
#> TCGA-02-0079-01A-03 5 0.0794 0.8055 0.000 0.028 0.000 0.000 0.972
#> TCGA-02-0085-01A-01 4 0.0609 0.7659 0.000 0.020 0.000 0.980 0.000
#> TCGA-02-0086-01A-01 2 0.0162 0.8998 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0099-01A-01 3 0.5778 0.0982 0.000 0.452 0.460 0.088 0.000
#> TCGA-02-0106-01A-01 2 0.0162 0.8998 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0107-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.1410 0.8723 0.000 0.940 0.000 0.000 0.060
#> TCGA-02-0326-01A-01 5 0.0162 0.8142 0.000 0.000 0.004 0.000 0.996
#> TCGA-02-0337-01A-01 2 0.4440 0.1639 0.000 0.528 0.004 0.000 0.468
#> TCGA-06-0122-01A-01 3 0.0566 0.8950 0.012 0.004 0.984 0.000 0.000
#> TCGA-06-0124-01A-01 3 0.0609 0.8906 0.000 0.020 0.980 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.0798 0.8942 0.016 0.008 0.976 0.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.4114 0.6099 0.000 0.712 0.016 0.000 0.272
#> TCGA-06-0152-01A-02 5 0.0162 0.8142 0.000 0.000 0.004 0.000 0.996
#> TCGA-06-0154-01A-02 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.3520 0.8240 0.040 0.040 0.856 0.064 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0184-01A-01 4 0.4638 0.4575 0.000 0.324 0.000 0.648 0.028
#> TCGA-06-0189-01A-05 2 0.1732 0.8575 0.000 0.920 0.000 0.000 0.080
#> TCGA-06-0190-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0510 0.8961 0.000 0.984 0.000 0.000 0.016
#> TCGA-06-0210-01A-01 2 0.0162 0.8998 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0397-01A-01 2 0.2813 0.7595 0.000 0.832 0.168 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.2605 0.7830 0.000 0.852 0.148 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.0510 0.8961 0.000 0.984 0.000 0.000 0.016
#> TCGA-06-0645-01A-01 2 0.1270 0.8782 0.000 0.948 0.000 0.000 0.052
#> TCGA-08-0346-01A-01 2 0.3837 0.5724 0.000 0.692 0.000 0.000 0.308
#> TCGA-08-0352-01A-01 2 0.8205 0.0335 0.000 0.372 0.128 0.220 0.280
#> TCGA-08-0360-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0390-01A-01 5 0.5921 0.3523 0.000 0.296 0.000 0.136 0.568
#> TCGA-08-0392-01A-01 5 0.4307 -0.0596 0.000 0.500 0.000 0.000 0.500
#> TCGA-08-0509-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.0613 0.8937 0.004 0.008 0.984 0.004 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9006 0.000 1.000 0.000 0.000 0.000
#> TCGA-12-0620-01A-01 5 0.0703 0.8079 0.000 0.024 0.000 0.000 0.976
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.0363 0.91870 0.988 0.000 0.000 0.000 0.000 0.012
#> TCGA-02-0010-01A-01 1 0.0260 0.92009 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0964 0.91510 0.968 0.000 0.012 0.000 0.004 0.016
#> TCGA-02-0014-01A-01 1 0.0146 0.92055 0.996 0.000 0.004 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0146 0.91982 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-02-0026-01B-01 1 0.0291 0.92064 0.992 0.000 0.004 0.000 0.000 0.004
#> TCGA-02-0028-01A-01 1 0.0458 0.91833 0.984 0.000 0.016 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0260 0.92009 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 6 0.1700 0.53285 0.004 0.000 0.000 0.080 0.000 0.916
#> TCGA-02-0048-01A-01 1 0.0622 0.92034 0.980 0.000 0.008 0.000 0.000 0.012
#> TCGA-02-0060-01A-01 6 0.4114 0.04074 0.460 0.000 0.000 0.004 0.004 0.532
#> TCGA-02-0069-01A-01 1 0.0363 0.91944 0.988 0.000 0.012 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0458 0.91825 0.984 0.000 0.016 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.5902 0.47819 0.584 0.000 0.076 0.000 0.264 0.076
#> TCGA-02-0084-01A-03 5 0.2134 0.67901 0.000 0.000 0.000 0.044 0.904 0.052
#> TCGA-02-0087-01A-01 5 0.5800 0.38655 0.252 0.000 0.048 0.004 0.604 0.092
#> TCGA-02-0104-01A-01 4 0.4334 0.49740 0.020 0.000 0.000 0.720 0.220 0.040
#> TCGA-02-0114-01A-01 1 0.0260 0.92009 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0146 0.92055 0.996 0.000 0.004 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.3790 0.60455 0.000 0.004 0.000 0.264 0.716 0.016
#> TCGA-02-0325-01A-01 3 0.5001 0.01379 0.460 0.000 0.492 0.004 0.024 0.020
#> TCGA-02-0338-01A-01 1 0.0146 0.92055 0.996 0.000 0.004 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0146 0.92055 0.996 0.000 0.004 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.5311 0.51533 0.616 0.000 0.004 0.004 0.248 0.128
#> TCGA-02-0439-01A-01 6 0.4694 0.16550 0.000 0.000 0.000 0.052 0.376 0.572
#> TCGA-02-0440-01A-01 1 0.0508 0.91802 0.984 0.000 0.000 0.004 0.000 0.012
#> TCGA-02-0446-01A-01 6 0.3383 0.42262 0.268 0.000 0.000 0.004 0.000 0.728
#> TCGA-06-0128-01A-01 1 0.2320 0.82501 0.864 0.000 0.132 0.000 0.000 0.004
#> TCGA-06-0129-01A-01 1 0.2092 0.83510 0.876 0.000 0.124 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.2375 0.86642 0.896 0.000 0.068 0.000 0.016 0.020
#> TCGA-06-0156-01A-01 1 0.2614 0.85629 0.884 0.044 0.000 0.012 0.000 0.060
#> TCGA-06-0166-01A-01 6 0.7723 0.00253 0.164 0.268 0.000 0.260 0.004 0.304
#> TCGA-06-0174-01A-01 1 0.0508 0.91802 0.984 0.000 0.000 0.004 0.000 0.012
#> TCGA-06-0177-01A-01 1 0.1708 0.89144 0.932 0.000 0.000 0.004 0.040 0.024
#> TCGA-06-0238-01A-02 5 0.4395 0.37786 0.000 0.000 0.000 0.404 0.568 0.028
#> TCGA-06-0241-01A-02 1 0.0508 0.91802 0.984 0.000 0.000 0.004 0.000 0.012
#> TCGA-06-0410-01A-01 1 0.4015 0.41043 0.616 0.000 0.000 0.372 0.000 0.012
#> TCGA-06-0413-01A-01 1 0.0146 0.92055 0.996 0.000 0.004 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0363 0.91870 0.988 0.000 0.000 0.000 0.000 0.012
#> TCGA-06-0646-01A-01 1 0.4458 0.74107 0.768 0.004 0.032 0.004 0.124 0.068
#> TCGA-06-0648-01A-01 5 0.5022 0.58193 0.040 0.000 0.000 0.256 0.656 0.048
#> TCGA-08-0245-01A-01 1 0.0405 0.91914 0.988 0.000 0.000 0.004 0.000 0.008
#> TCGA-08-0344-01A-01 1 0.4137 0.67347 0.732 0.000 0.000 0.040 0.012 0.216
#> TCGA-08-0347-01A-01 6 0.3353 0.45959 0.004 0.000 0.000 0.032 0.160 0.804
#> TCGA-08-0348-01A-01 1 0.2034 0.88630 0.912 0.000 0.000 0.004 0.024 0.060
#> TCGA-08-0350-01A-01 5 0.2288 0.68649 0.004 0.000 0.000 0.072 0.896 0.028
#> TCGA-08-0353-01A-01 1 0.2214 0.85758 0.892 0.000 0.092 0.000 0.004 0.012
#> TCGA-08-0359-01A-01 6 0.4678 0.45229 0.124 0.000 0.000 0.132 0.020 0.724
#> TCGA-08-0385-01A-01 5 0.3936 0.59547 0.004 0.000 0.000 0.276 0.700 0.020
#> TCGA-08-0517-01A-01 1 0.0790 0.91338 0.968 0.000 0.000 0.000 0.000 0.032
#> TCGA-08-0524-01A-01 1 0.0291 0.91967 0.992 0.000 0.000 0.004 0.000 0.004
#> TCGA-12-0616-01A-01 5 0.5993 0.28642 0.128 0.000 0.000 0.372 0.476 0.024
#> TCGA-12-0618-01A-01 1 0.0935 0.91245 0.964 0.000 0.000 0.004 0.000 0.032
#> TCGA-02-0089-01A-01 6 0.2730 0.51189 0.000 0.000 0.000 0.192 0.000 0.808
#> TCGA-02-0113-01A-01 4 0.6761 -0.07094 0.000 0.020 0.260 0.432 0.016 0.272
#> TCGA-02-0115-01A-01 6 0.2454 0.52351 0.000 0.000 0.000 0.160 0.000 0.840
#> TCGA-02-0451-01A-01 6 0.2562 0.51901 0.000 0.000 0.000 0.172 0.000 0.828
#> TCGA-06-0132-01A-02 6 0.3634 0.38409 0.000 0.000 0.000 0.356 0.000 0.644
#> TCGA-06-0133-01A-02 4 0.3797 -0.02825 0.000 0.000 0.000 0.580 0.000 0.420
#> TCGA-06-0138-01A-02 4 0.2527 0.66893 0.000 0.000 0.000 0.868 0.108 0.024
#> TCGA-06-0160-01A-01 6 0.3578 0.39745 0.000 0.000 0.000 0.340 0.000 0.660
#> TCGA-06-0162-01A-01 4 0.2618 0.66829 0.000 0.000 0.000 0.860 0.116 0.024
#> TCGA-06-0167-01A-01 6 0.3578 0.39745 0.000 0.000 0.000 0.340 0.000 0.660
#> TCGA-06-0171-01A-02 4 0.2962 0.64308 0.000 0.000 0.000 0.848 0.068 0.084
#> TCGA-06-0173-01A-01 6 0.4362 0.44028 0.016 0.008 0.020 0.256 0.000 0.700
#> TCGA-06-0179-01A-02 6 0.3747 0.32833 0.000 0.000 0.000 0.396 0.000 0.604
#> TCGA-06-0182-01A-01 4 0.1814 0.66144 0.000 0.000 0.000 0.900 0.100 0.000
#> TCGA-06-0185-01A-01 4 0.3331 0.54927 0.000 0.000 0.004 0.816 0.044 0.136
#> TCGA-06-0195-01B-01 6 0.3782 0.30160 0.000 0.000 0.000 0.412 0.000 0.588
#> TCGA-06-0208-01B-01 4 0.2768 0.53607 0.000 0.000 0.000 0.832 0.012 0.156
#> TCGA-06-0214-01A-02 6 0.3747 0.27882 0.000 0.000 0.000 0.396 0.000 0.604
#> TCGA-06-0219-01A-01 4 0.2618 0.66829 0.000 0.000 0.000 0.860 0.116 0.024
#> TCGA-06-0221-01A-01 4 0.2748 0.66303 0.000 0.000 0.000 0.848 0.128 0.024
#> TCGA-06-0237-01A-02 4 0.2794 0.65379 0.000 0.000 0.000 0.860 0.080 0.060
#> TCGA-06-0240-01A-02 6 0.3851 0.20572 0.000 0.000 0.000 0.460 0.000 0.540
#> TCGA-08-0349-01A-01 4 0.5636 0.31835 0.000 0.000 0.000 0.516 0.176 0.308
#> TCGA-08-0380-01A-01 4 0.5107 0.30491 0.000 0.004 0.004 0.616 0.088 0.288
#> TCGA-08-0386-01A-01 6 0.5505 0.39790 0.036 0.000 0.180 0.104 0.012 0.668
#> TCGA-08-0520-01A-01 4 0.2662 0.66545 0.000 0.000 0.000 0.856 0.120 0.024
#> TCGA-02-0007-01A-01 3 0.3051 0.77232 0.024 0.000 0.856 0.032 0.000 0.088
#> TCGA-02-0009-01A-01 3 0.0146 0.83733 0.004 0.000 0.996 0.000 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.4892 0.50111 0.000 0.000 0.628 0.000 0.272 0.100
#> TCGA-02-0021-01A-01 3 0.0291 0.83697 0.004 0.000 0.992 0.004 0.000 0.000
#> TCGA-02-0023-01B-01 5 0.2201 0.68834 0.000 0.000 0.000 0.076 0.896 0.028
#> TCGA-02-0027-01A-01 3 0.0810 0.83327 0.008 0.000 0.976 0.004 0.004 0.008
#> TCGA-02-0038-01A-01 3 0.5383 0.49797 0.000 0.004 0.604 0.112 0.008 0.272
#> TCGA-02-0043-01A-01 3 0.0146 0.83733 0.004 0.000 0.996 0.000 0.000 0.000
#> TCGA-02-0070-01A-01 5 0.4672 0.36405 0.000 0.012 0.316 0.004 0.636 0.032
#> TCGA-02-0102-01A-01 3 0.0146 0.83733 0.004 0.000 0.996 0.000 0.000 0.000
#> TCGA-02-0260-01A-03 5 0.4722 -0.10447 0.012 0.000 0.476 0.000 0.488 0.024
#> TCGA-02-0269-01B-01 5 0.1710 0.67141 0.000 0.000 0.020 0.016 0.936 0.028
#> TCGA-02-0285-01A-01 5 0.1875 0.68368 0.000 0.000 0.020 0.032 0.928 0.020
#> TCGA-02-0289-01A-01 5 0.3510 0.61034 0.000 0.000 0.096 0.032 0.828 0.044
#> TCGA-02-0290-01A-01 5 0.3482 0.55820 0.000 0.000 0.000 0.316 0.684 0.000
#> TCGA-02-0317-01A-01 5 0.1092 0.68209 0.000 0.000 0.000 0.020 0.960 0.020
#> TCGA-02-0333-01A-02 5 0.2095 0.66320 0.000 0.000 0.040 0.016 0.916 0.028
#> TCGA-02-0422-01A-01 5 0.5931 0.44365 0.000 0.000 0.028 0.212 0.572 0.188
#> TCGA-02-0430-01A-01 3 0.1371 0.82187 0.004 0.000 0.948 0.004 0.040 0.004
#> TCGA-06-0125-01A-01 3 0.0146 0.83733 0.004 0.000 0.996 0.000 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.0146 0.83733 0.004 0.000 0.996 0.000 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.0363 0.83493 0.000 0.000 0.988 0.000 0.000 0.012
#> TCGA-06-0145-01A-04 3 0.0000 0.83672 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.0891 0.82987 0.000 0.000 0.968 0.000 0.024 0.008
#> TCGA-06-0187-01A-01 3 0.5272 0.56816 0.000 0.004 0.652 0.100 0.020 0.224
#> TCGA-06-0211-01B-01 4 0.4784 0.44652 0.000 0.000 0.056 0.724 0.060 0.160
#> TCGA-06-0402-01A-01 3 0.0146 0.83733 0.004 0.000 0.996 0.000 0.000 0.000
#> TCGA-08-0246-01A-01 5 0.6897 0.35494 0.000 0.112 0.004 0.184 0.512 0.188
#> TCGA-08-0354-01A-01 5 0.4046 0.49263 0.000 0.004 0.000 0.368 0.620 0.008
#> TCGA-08-0355-01A-01 5 0.1320 0.68760 0.000 0.000 0.000 0.036 0.948 0.016
#> TCGA-08-0357-01A-01 5 0.5748 0.35452 0.000 0.000 0.024 0.124 0.564 0.288
#> TCGA-08-0358-01A-01 5 0.3023 0.63159 0.000 0.000 0.000 0.232 0.768 0.000
#> TCGA-08-0375-01A-01 3 0.5334 0.35637 0.060 0.000 0.572 0.004 0.344 0.020
#> TCGA-08-0511-01A-01 6 0.5574 0.18912 0.000 0.000 0.320 0.060 0.048 0.572
#> TCGA-08-0514-01A-01 3 0.6007 0.52935 0.000 0.000 0.600 0.088 0.096 0.216
#> TCGA-08-0518-01A-01 3 0.0146 0.83733 0.004 0.000 0.996 0.000 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.2541 0.79854 0.000 0.000 0.892 0.032 0.052 0.024
#> TCGA-08-0531-01A-01 3 0.7442 0.10984 0.000 0.000 0.324 0.128 0.308 0.240
#> TCGA-02-0057-01A-01 3 0.4078 0.61933 0.000 0.008 0.700 0.024 0.000 0.268
#> TCGA-02-0004-01A-01 2 0.1493 0.84362 0.000 0.936 0.000 0.056 0.004 0.004
#> TCGA-02-0006-01B-01 2 0.6609 -0.03291 0.000 0.428 0.168 0.052 0.000 0.352
#> TCGA-02-0025-01A-01 2 0.3707 0.75192 0.000 0.796 0.000 0.100 0.100 0.004
#> TCGA-02-0033-01A-01 2 0.0000 0.85992 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0146 0.85920 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0039-01A-01 2 0.5235 0.50791 0.000 0.628 0.004 0.044 0.284 0.040
#> TCGA-02-0051-01A-01 2 0.2355 0.81081 0.000 0.876 0.000 0.112 0.008 0.004
#> TCGA-02-0054-01A-01 6 0.7056 0.05517 0.000 0.324 0.256 0.068 0.000 0.352
#> TCGA-02-0055-01A-01 2 0.1285 0.84688 0.000 0.944 0.000 0.052 0.000 0.004
#> TCGA-02-0059-01A-01 2 0.4258 0.67176 0.000 0.724 0.000 0.204 0.068 0.004
#> TCGA-02-0064-01A-01 3 0.1674 0.79999 0.000 0.068 0.924 0.004 0.000 0.004
#> TCGA-02-0075-01A-01 3 0.0837 0.83012 0.000 0.020 0.972 0.004 0.000 0.004
#> TCGA-02-0079-01A-03 5 0.3377 0.66097 0.000 0.056 0.000 0.136 0.808 0.000
#> TCGA-02-0085-01A-01 6 0.3236 0.50959 0.000 0.024 0.000 0.180 0.000 0.796
#> TCGA-02-0086-01A-01 2 0.2442 0.81558 0.000 0.884 0.000 0.068 0.000 0.048
#> TCGA-02-0099-01A-01 2 0.6936 -0.19324 0.000 0.336 0.332 0.052 0.000 0.280
#> TCGA-02-0106-01A-01 2 0.0603 0.85695 0.000 0.980 0.000 0.016 0.000 0.004
#> TCGA-02-0107-01A-01 2 0.0363 0.85709 0.000 0.988 0.000 0.000 0.000 0.012
#> TCGA-02-0111-01A-01 2 0.3395 0.76986 0.000 0.816 0.000 0.124 0.056 0.004
#> TCGA-02-0326-01A-01 5 0.1765 0.68709 0.000 0.000 0.000 0.096 0.904 0.000
#> TCGA-02-0337-01A-01 5 0.4407 -0.09493 0.000 0.480 0.000 0.024 0.496 0.000
#> TCGA-06-0122-01A-01 3 0.0436 0.83610 0.004 0.000 0.988 0.004 0.000 0.004
#> TCGA-06-0124-01A-01 3 0.0837 0.83012 0.000 0.020 0.972 0.004 0.000 0.004
#> TCGA-06-0130-01A-01 2 0.0000 0.85992 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.85992 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.0912 0.83246 0.004 0.012 0.972 0.004 0.000 0.008
#> TCGA-06-0147-01A-01 2 0.0146 0.85928 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-06-0149-01A-05 2 0.6019 0.22234 0.000 0.504 0.004 0.052 0.368 0.072
#> TCGA-06-0152-01A-02 5 0.1958 0.68657 0.000 0.000 0.000 0.100 0.896 0.004
#> TCGA-06-0154-01A-02 2 0.0000 0.85992 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.85992 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.5538 0.48811 0.032 0.028 0.596 0.032 0.000 0.312
#> TCGA-06-0176-01A-03 2 0.0000 0.85992 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0184-01A-01 4 0.5491 0.18844 0.000 0.332 0.000 0.524 0.000 0.144
#> TCGA-06-0189-01A-05 2 0.3650 0.70326 0.000 0.756 0.000 0.216 0.024 0.004
#> TCGA-06-0190-01A-01 2 0.0000 0.85992 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0291 0.85881 0.000 0.992 0.000 0.004 0.000 0.004
#> TCGA-06-0197-01A-02 2 0.2624 0.78500 0.000 0.844 0.000 0.148 0.004 0.004
#> TCGA-06-0210-01A-01 2 0.0777 0.85621 0.000 0.972 0.000 0.024 0.000 0.004
#> TCGA-06-0397-01A-01 2 0.2624 0.75561 0.000 0.844 0.148 0.004 0.000 0.004
#> TCGA-06-0409-01A-02 2 0.0260 0.85810 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-06-0412-01A-01 2 0.2779 0.76215 0.000 0.856 0.120 0.004 0.004 0.016
#> TCGA-06-0644-01A-02 2 0.1155 0.85154 0.000 0.956 0.000 0.036 0.004 0.004
#> TCGA-06-0645-01A-01 2 0.1934 0.83285 0.000 0.916 0.000 0.040 0.044 0.000
#> TCGA-08-0346-01A-01 2 0.4736 0.60425 0.000 0.680 0.000 0.104 0.212 0.004
#> TCGA-08-0352-01A-01 6 0.6879 0.28856 0.000 0.220 0.132 0.004 0.132 0.512
#> TCGA-08-0360-01A-01 2 0.0146 0.85920 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-08-0390-01A-01 4 0.6530 -0.05301 0.000 0.308 0.000 0.372 0.300 0.020
#> TCGA-08-0392-01A-01 2 0.6069 0.11877 0.000 0.444 0.000 0.316 0.236 0.004
#> TCGA-08-0509-01A-01 2 0.0260 0.85810 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-08-0510-01A-01 3 0.2089 0.80286 0.004 0.004 0.908 0.012 0.000 0.072
#> TCGA-08-0512-01A-01 2 0.0146 0.85920 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-08-0522-01A-01 2 0.0000 0.85992 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.85992 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0620-01A-01 5 0.4049 0.60655 0.000 0.032 0.000 0.256 0.708 0.004
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> CV:skmeans 165 1.05e-10 2
#> CV:skmeans 132 6.87e-29 3
#> CV:skmeans 137 1.85e-51 4
#> CV:skmeans 148 1.97e-59 5
#> CV:skmeans 126 1.53e-51 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "pam"]
# you can also extract it by
# res = res_list["CV:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.515 0.850 0.904 0.3935 0.613 0.613
#> 3 3 0.522 0.712 0.856 0.5395 0.752 0.608
#> 4 4 0.725 0.824 0.900 0.1800 0.851 0.644
#> 5 5 0.800 0.837 0.910 0.0640 0.942 0.800
#> 6 6 0.832 0.841 0.925 0.0211 0.993 0.971
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.800 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0011-01B-01 1 0.7745 0.865 0.772 0.228
#> TCGA-02-0014-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0024-01B-01 1 0.2603 0.821 0.956 0.044
#> TCGA-02-0026-01B-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0028-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0046-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0047-01A-01 1 0.0000 0.800 1.000 0.000
#> TCGA-02-0048-01A-01 1 0.7674 0.865 0.776 0.224
#> TCGA-02-0060-01A-01 1 0.1633 0.813 0.976 0.024
#> TCGA-02-0069-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0074-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0080-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0084-01A-03 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0087-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0104-01A-01 2 0.8763 0.684 0.296 0.704
#> TCGA-02-0114-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0281-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0321-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0325-01A-01 1 0.9815 0.593 0.580 0.420
#> TCGA-02-0338-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0339-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0432-01A-02 1 0.4815 0.843 0.896 0.104
#> TCGA-02-0439-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0440-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-02-0446-01A-01 1 0.0000 0.800 1.000 0.000
#> TCGA-06-0128-01A-01 2 0.9358 0.304 0.352 0.648
#> TCGA-06-0129-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-06-0146-01A-01 1 0.7950 0.861 0.760 0.240
#> TCGA-06-0156-01A-01 1 0.0672 0.805 0.992 0.008
#> TCGA-06-0166-01A-01 1 0.5842 0.807 0.860 0.140
#> TCGA-06-0174-01A-01 1 0.6438 0.858 0.836 0.164
#> TCGA-06-0177-01A-01 1 0.9933 0.521 0.548 0.452
#> TCGA-06-0238-01A-02 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0241-01A-02 1 0.0938 0.808 0.988 0.012
#> TCGA-06-0410-01A-01 1 0.6531 0.727 0.832 0.168
#> TCGA-06-0413-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-06-0414-01A-01 1 0.7602 0.866 0.780 0.220
#> TCGA-06-0646-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0648-01A-01 1 0.9129 0.675 0.672 0.328
#> TCGA-08-0245-01A-01 1 0.7815 0.865 0.768 0.232
#> TCGA-08-0344-01A-01 1 0.0000 0.800 1.000 0.000
#> TCGA-08-0347-01A-01 2 0.0672 0.910 0.008 0.992
#> TCGA-08-0348-01A-01 1 0.7815 0.865 0.768 0.232
#> TCGA-08-0350-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0353-01A-01 2 0.1633 0.894 0.024 0.976
#> TCGA-08-0359-01A-01 1 0.1184 0.809 0.984 0.016
#> TCGA-08-0385-01A-01 2 0.9248 0.603 0.340 0.660
#> TCGA-08-0517-01A-01 1 0.7883 0.864 0.764 0.236
#> TCGA-08-0524-01A-01 1 0.7299 0.865 0.796 0.204
#> TCGA-12-0616-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-12-0618-01A-01 1 0.6887 0.862 0.816 0.184
#> TCGA-02-0089-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-02-0113-01A-01 2 0.1184 0.906 0.016 0.984
#> TCGA-02-0115-01A-01 1 0.3431 0.783 0.936 0.064
#> TCGA-02-0451-01A-01 1 0.6887 0.687 0.816 0.184
#> TCGA-06-0132-01A-02 2 0.7950 0.748 0.240 0.760
#> TCGA-06-0133-01A-02 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0138-01A-02 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0160-01A-01 1 0.0000 0.800 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0167-01A-01 1 0.0000 0.800 1.000 0.000
#> TCGA-06-0171-01A-02 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0173-01A-01 2 0.7815 0.756 0.232 0.768
#> TCGA-06-0179-01A-02 2 0.9963 0.339 0.464 0.536
#> TCGA-06-0182-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0185-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0195-01B-01 1 0.0000 0.800 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0214-01A-02 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0219-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0221-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0237-01A-02 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0240-01A-02 2 0.8144 0.737 0.252 0.748
#> TCGA-08-0349-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-08-0380-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-08-0386-01A-01 2 0.5946 0.827 0.144 0.856
#> TCGA-08-0520-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-02-0007-01A-01 2 0.4815 0.807 0.104 0.896
#> TCGA-02-0009-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0016-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0021-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0023-01B-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.8144 0.851 0.748 0.252
#> TCGA-02-0038-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0043-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0070-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0102-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0260-01A-03 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0269-01B-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0285-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0289-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0290-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0317-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0333-01A-02 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0422-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0430-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0125-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0126-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0137-01A-03 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0145-01A-04 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0148-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0187-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0211-01B-01 2 0.1843 0.899 0.028 0.972
#> TCGA-06-0402-01A-01 2 0.2423 0.878 0.040 0.960
#> TCGA-08-0246-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.1414 0.904 0.020 0.980
#> TCGA-08-0355-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0357-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0358-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0375-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0511-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0514-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0529-01A-02 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0531-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0057-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.6801 0.796 0.180 0.820
#> TCGA-02-0006-01B-01 2 0.0672 0.910 0.008 0.992
#> TCGA-02-0025-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.3431 0.877 0.064 0.936
#> TCGA-02-0054-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-02-0059-01A-01 2 0.7528 0.768 0.216 0.784
#> TCGA-02-0064-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.7815 0.755 0.232 0.768
#> TCGA-02-0086-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.4161 0.866 0.084 0.916
#> TCGA-02-0106-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.6973 0.790 0.188 0.812
#> TCGA-02-0111-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-02-0337-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.5178 0.785 0.116 0.884
#> TCGA-06-0147-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0189-01A-05 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0190-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.7883 0.752 0.236 0.764
#> TCGA-06-0210-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.914 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.7815 0.755 0.232 0.768
#> TCGA-08-0392-01A-01 2 0.7883 0.752 0.236 0.764
#> TCGA-08-0509-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0376 0.911 0.004 0.996
#> TCGA-08-0512-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.914 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.914 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.1289 0.8271 0.968 0.032 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.1289 0.8271 0.968 0.032 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 2 0.5529 0.4793 0.296 0.704 0.000
#> TCGA-02-0048-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.2537 0.7959 0.920 0.080 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0084-01A-03 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0087-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0104-01A-01 2 0.6887 0.6810 0.060 0.704 0.236
#> TCGA-02-0114-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.4062 0.7391 0.836 0.000 0.164
#> TCGA-02-0321-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0325-01A-01 1 0.5397 0.5789 0.720 0.000 0.280
#> TCGA-02-0338-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.2625 0.8085 0.916 0.000 0.084
#> TCGA-02-0432-01A-02 1 0.7653 0.6158 0.684 0.176 0.140
#> TCGA-02-0439-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0440-01A-01 1 0.2625 0.8080 0.916 0.000 0.084
#> TCGA-02-0446-01A-01 1 0.4235 0.7063 0.824 0.176 0.000
#> TCGA-06-0128-01A-01 1 0.7063 0.0330 0.516 0.020 0.464
#> TCGA-06-0129-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.2537 0.8124 0.920 0.000 0.080
#> TCGA-06-0156-01A-01 2 0.6169 0.3730 0.360 0.636 0.004
#> TCGA-06-0166-01A-01 1 0.8526 0.3769 0.572 0.308 0.120
#> TCGA-06-0174-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.6305 0.1719 0.516 0.000 0.484
#> TCGA-06-0238-01A-02 2 0.5529 0.6926 0.000 0.704 0.296
#> TCGA-06-0241-01A-02 1 0.3619 0.7511 0.864 0.136 0.000
#> TCGA-06-0410-01A-01 2 0.7958 0.2569 0.392 0.544 0.064
#> TCGA-06-0413-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.0424 0.8384 0.008 0.000 0.992
#> TCGA-06-0648-01A-01 1 0.7600 0.4571 0.600 0.056 0.344
#> TCGA-08-0245-01A-01 1 0.4178 0.7323 0.828 0.000 0.172
#> TCGA-08-0344-01A-01 1 0.6095 0.3159 0.608 0.392 0.000
#> TCGA-08-0347-01A-01 3 0.0424 0.8373 0.000 0.008 0.992
#> TCGA-08-0348-01A-01 1 0.4504 0.7113 0.804 0.000 0.196
#> TCGA-08-0350-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-08-0353-01A-01 3 0.3551 0.7663 0.132 0.000 0.868
#> TCGA-08-0359-01A-01 1 0.5695 0.7383 0.804 0.120 0.076
#> TCGA-08-0385-01A-01 3 0.8863 -0.0618 0.128 0.360 0.512
#> TCGA-08-0517-01A-01 1 0.1031 0.8375 0.976 0.000 0.024
#> TCGA-08-0524-01A-01 1 0.4645 0.7281 0.816 0.008 0.176
#> TCGA-12-0616-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-12-0618-01A-01 1 0.0000 0.8435 1.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.5529 0.6926 0.000 0.704 0.296
#> TCGA-02-0113-01A-01 3 0.3690 0.7550 0.016 0.100 0.884
#> TCGA-02-0115-01A-01 2 0.2200 0.6663 0.056 0.940 0.004
#> TCGA-02-0451-01A-01 2 0.6684 0.4848 0.292 0.676 0.032
#> TCGA-06-0132-01A-02 2 0.0000 0.6765 0.000 1.000 0.000
#> TCGA-06-0133-01A-02 2 0.5058 0.7053 0.000 0.756 0.244
#> TCGA-06-0138-01A-02 2 0.5529 0.6926 0.000 0.704 0.296
#> TCGA-06-0160-01A-01 2 0.5529 0.4793 0.296 0.704 0.000
#> TCGA-06-0162-01A-01 2 0.0000 0.6765 0.000 1.000 0.000
#> TCGA-06-0167-01A-01 2 0.5529 0.4793 0.296 0.704 0.000
#> TCGA-06-0171-01A-02 2 0.5529 0.6926 0.000 0.704 0.296
#> TCGA-06-0173-01A-01 2 0.5785 0.6884 0.004 0.696 0.300
#> TCGA-06-0179-01A-02 2 0.0000 0.6765 0.000 1.000 0.000
#> TCGA-06-0182-01A-01 2 0.5529 0.6926 0.000 0.704 0.296
#> TCGA-06-0185-01A-01 2 0.5529 0.6926 0.000 0.704 0.296
#> TCGA-06-0195-01B-01 2 0.5529 0.4793 0.296 0.704 0.000
#> TCGA-06-0208-01B-01 2 0.5497 0.6940 0.000 0.708 0.292
#> TCGA-06-0214-01A-02 2 0.5529 0.6926 0.000 0.704 0.296
#> TCGA-06-0219-01A-01 2 0.0000 0.6765 0.000 1.000 0.000
#> TCGA-06-0221-01A-01 2 0.5529 0.6926 0.000 0.704 0.296
#> TCGA-06-0237-01A-02 2 0.5529 0.6926 0.000 0.704 0.296
#> TCGA-06-0240-01A-02 2 0.1525 0.6903 0.004 0.964 0.032
#> TCGA-08-0349-01A-01 2 0.5529 0.6926 0.000 0.704 0.296
#> TCGA-08-0380-01A-01 2 0.0000 0.6765 0.000 1.000 0.000
#> TCGA-08-0386-01A-01 3 0.6663 0.6369 0.156 0.096 0.748
#> TCGA-08-0520-01A-01 2 0.4796 0.7080 0.000 0.780 0.220
#> TCGA-02-0007-01A-01 3 0.5285 0.6683 0.244 0.004 0.752
#> TCGA-02-0009-01A-01 3 0.4555 0.6894 0.200 0.000 0.800
#> TCGA-02-0016-01A-01 3 0.1163 0.8306 0.028 0.000 0.972
#> TCGA-02-0021-01A-01 3 0.1289 0.8286 0.032 0.000 0.968
#> TCGA-02-0023-01B-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.0747 0.8375 0.984 0.000 0.016
#> TCGA-02-0038-01A-01 3 0.0747 0.8355 0.016 0.000 0.984
#> TCGA-02-0043-01A-01 3 0.4504 0.6931 0.196 0.000 0.804
#> TCGA-02-0070-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0102-01A-01 3 0.4654 0.6816 0.208 0.000 0.792
#> TCGA-02-0260-01A-03 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0269-01B-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0285-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0289-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0290-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0317-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0333-01A-02 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0422-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0430-01A-01 3 0.1289 0.8286 0.032 0.000 0.968
#> TCGA-06-0125-01A-01 3 0.4605 0.6856 0.204 0.000 0.796
#> TCGA-06-0126-01A-01 3 0.4504 0.6931 0.196 0.000 0.804
#> TCGA-06-0137-01A-03 3 0.2878 0.7894 0.096 0.000 0.904
#> TCGA-06-0145-01A-04 3 0.1289 0.8286 0.032 0.000 0.968
#> TCGA-06-0148-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-06-0187-01A-01 3 0.1163 0.8305 0.028 0.000 0.972
#> TCGA-06-0211-01B-01 3 0.4291 0.6416 0.000 0.180 0.820
#> TCGA-06-0402-01A-01 3 0.5016 0.6398 0.240 0.000 0.760
#> TCGA-08-0246-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-08-0354-01A-01 3 0.0892 0.8312 0.000 0.020 0.980
#> TCGA-08-0355-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-08-0357-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-08-0358-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-08-0375-01A-01 3 0.1289 0.8286 0.032 0.000 0.968
#> TCGA-08-0511-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-08-0514-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-08-0518-01A-01 3 0.2711 0.7973 0.088 0.000 0.912
#> TCGA-08-0529-01A-02 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-08-0531-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0057-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0004-01A-01 3 0.6299 0.3761 0.000 0.476 0.524
#> TCGA-02-0006-01B-01 3 0.7180 0.6492 0.060 0.268 0.672
#> TCGA-02-0025-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-02-0033-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-02-0034-01A-01 3 0.5016 0.7072 0.000 0.240 0.760
#> TCGA-02-0039-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-02-0051-01A-01 3 0.5948 0.5942 0.000 0.360 0.640
#> TCGA-02-0054-01A-01 3 0.5928 0.6594 0.008 0.296 0.696
#> TCGA-02-0055-01A-01 2 0.1031 0.6749 0.000 0.976 0.024
#> TCGA-02-0059-01A-01 2 0.6079 0.0429 0.000 0.612 0.388
#> TCGA-02-0064-01A-01 3 0.0747 0.8356 0.016 0.000 0.984
#> TCGA-02-0075-01A-01 3 0.5098 0.6351 0.248 0.000 0.752
#> TCGA-02-0079-01A-03 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.6126 0.5521 0.000 0.600 0.400
#> TCGA-02-0086-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-02-0099-01A-01 2 0.6944 -0.2523 0.016 0.516 0.468
#> TCGA-02-0106-01A-01 3 0.0424 0.8387 0.000 0.008 0.992
#> TCGA-02-0107-01A-01 2 0.1753 0.6656 0.000 0.952 0.048
#> TCGA-02-0111-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-02-0326-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-02-0337-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-06-0122-01A-01 3 0.4974 0.6534 0.236 0.000 0.764
#> TCGA-06-0124-01A-01 3 0.1289 0.8286 0.032 0.000 0.968
#> TCGA-06-0130-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-06-0139-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-06-0143-01A-01 3 0.4504 0.6885 0.196 0.000 0.804
#> TCGA-06-0147-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-06-0149-01A-05 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-06-0152-01A-02 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-06-0154-01A-02 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-06-0164-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-06-0175-01A-01 3 0.0747 0.8355 0.016 0.000 0.984
#> TCGA-06-0176-01A-03 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-06-0184-01A-01 2 0.0000 0.6765 0.000 1.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.6765 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-06-0194-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-06-0197-01A-02 2 0.1289 0.6731 0.000 0.968 0.032
#> TCGA-06-0210-01A-01 3 0.1860 0.8223 0.000 0.052 0.948
#> TCGA-06-0397-01A-01 3 0.7564 0.6201 0.068 0.296 0.636
#> TCGA-06-0409-01A-02 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-06-0412-01A-01 3 0.0661 0.8391 0.008 0.004 0.988
#> TCGA-06-0644-01A-02 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-06-0645-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-08-0346-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-08-0352-01A-01 3 0.0000 0.8402 0.000 0.000 1.000
#> TCGA-08-0360-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-08-0390-01A-01 2 0.4235 0.5743 0.000 0.824 0.176
#> TCGA-08-0392-01A-01 2 0.2066 0.6613 0.000 0.940 0.060
#> TCGA-08-0509-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-08-0510-01A-01 3 0.5944 0.7552 0.088 0.120 0.792
#> TCGA-08-0512-01A-01 3 0.6357 0.6566 0.020 0.296 0.684
#> TCGA-08-0522-01A-01 3 0.5529 0.6647 0.000 0.296 0.704
#> TCGA-12-0619-01A-01 3 0.0424 0.8383 0.008 0.000 0.992
#> TCGA-12-0620-01A-01 3 0.5431 0.6744 0.000 0.284 0.716
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.0188 0.8630 0.996 0.000 0.000 0.004
#> TCGA-02-0010-01A-01 1 0.0188 0.8639 0.996 0.004 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.8643 1.000 0.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.8643 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0188 0.8630 0.996 0.000 0.000 0.004
#> TCGA-02-0026-01B-01 1 0.0469 0.8629 0.988 0.012 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0469 0.8629 0.988 0.012 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.8643 1.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-02-0048-01A-01 1 0.1637 0.8487 0.940 0.060 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.1867 0.8318 0.928 0.000 0.000 0.072
#> TCGA-02-0069-01A-01 1 0.0000 0.8643 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0336 0.8636 0.992 0.008 0.000 0.000
#> TCGA-02-0080-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0084-01A-03 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0087-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0104-01A-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-02-0114-01A-01 1 0.0000 0.8643 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.4685 0.7764 0.784 0.060 0.156 0.000
#> TCGA-02-0321-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0325-01A-01 1 0.5877 0.5951 0.656 0.068 0.276 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.8643 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.2402 0.8441 0.912 0.012 0.076 0.000
#> TCGA-02-0432-01A-02 1 0.6025 0.6834 0.688 0.000 0.140 0.172
#> TCGA-02-0439-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.1867 0.8449 0.928 0.000 0.072 0.000
#> TCGA-02-0446-01A-01 1 0.2921 0.7776 0.860 0.000 0.000 0.140
#> TCGA-06-0128-01A-01 1 0.7870 -0.0160 0.432 0.048 0.428 0.092
#> TCGA-06-0129-01A-01 1 0.1792 0.8467 0.932 0.068 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.3239 0.8393 0.880 0.052 0.068 0.000
#> TCGA-06-0156-01A-01 4 0.5504 0.6957 0.160 0.096 0.004 0.740
#> TCGA-06-0166-01A-01 1 0.7024 0.4878 0.572 0.008 0.120 0.300
#> TCGA-06-0174-01A-01 1 0.0000 0.8643 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.4992 0.2327 0.524 0.000 0.476 0.000
#> TCGA-06-0238-01A-02 4 0.0188 0.9487 0.000 0.000 0.004 0.996
#> TCGA-06-0241-01A-02 1 0.2530 0.8024 0.888 0.000 0.000 0.112
#> TCGA-06-0410-01A-01 4 0.4428 0.7749 0.116 0.004 0.064 0.816
#> TCGA-06-0413-01A-01 1 0.0000 0.8643 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.8643 1.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.0895 0.8954 0.004 0.020 0.976 0.000
#> TCGA-06-0648-01A-01 1 0.5755 0.5429 0.624 0.000 0.332 0.044
#> TCGA-08-0245-01A-01 1 0.4378 0.7763 0.796 0.040 0.164 0.000
#> TCGA-08-0344-01A-01 1 0.4790 0.4236 0.620 0.000 0.000 0.380
#> TCGA-08-0347-01A-01 3 0.0336 0.9018 0.000 0.000 0.992 0.008
#> TCGA-08-0348-01A-01 1 0.3172 0.7871 0.840 0.000 0.160 0.000
#> TCGA-08-0350-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-08-0353-01A-01 3 0.3679 0.8343 0.084 0.060 0.856 0.000
#> TCGA-08-0359-01A-01 1 0.4163 0.7965 0.828 0.000 0.076 0.096
#> TCGA-08-0385-01A-01 3 0.7024 0.2482 0.128 0.000 0.512 0.360
#> TCGA-08-0517-01A-01 1 0.1733 0.8597 0.948 0.028 0.024 0.000
#> TCGA-08-0524-01A-01 1 0.3257 0.7919 0.844 0.000 0.152 0.004
#> TCGA-12-0616-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.8643 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-02-0113-01A-01 3 0.5458 0.4107 0.004 0.016 0.612 0.368
#> TCGA-02-0115-01A-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-02-0451-01A-01 4 0.1042 0.9308 0.008 0.000 0.020 0.972
#> TCGA-06-0132-01A-02 4 0.0592 0.9444 0.000 0.016 0.000 0.984
#> TCGA-06-0133-01A-02 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 4 0.0592 0.9444 0.000 0.016 0.000 0.984
#> TCGA-06-0162-01A-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 4 0.0592 0.9444 0.000 0.016 0.000 0.984
#> TCGA-06-0171-01A-02 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 4 0.0804 0.9391 0.012 0.000 0.008 0.980
#> TCGA-06-0179-01A-02 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0195-01B-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0208-01B-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.0592 0.9444 0.000 0.016 0.000 0.984
#> TCGA-08-0349-01A-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.4406 0.6084 0.000 0.700 0.000 0.300
#> TCGA-08-0386-01A-01 3 0.6150 0.7275 0.132 0.044 0.732 0.092
#> TCGA-08-0520-01A-01 4 0.0000 0.9517 0.000 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.5400 0.7041 0.208 0.060 0.728 0.004
#> TCGA-02-0009-01A-01 3 0.4875 0.7607 0.160 0.068 0.772 0.000
#> TCGA-02-0016-01A-01 3 0.1305 0.8922 0.004 0.036 0.960 0.000
#> TCGA-02-0021-01A-01 3 0.1824 0.8809 0.004 0.060 0.936 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0027-01A-01 1 0.2142 0.8463 0.928 0.056 0.016 0.000
#> TCGA-02-0038-01A-01 3 0.1004 0.8965 0.004 0.024 0.972 0.000
#> TCGA-02-0043-01A-01 3 0.4875 0.7607 0.160 0.068 0.772 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0102-01A-01 3 0.4964 0.7524 0.168 0.068 0.764 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0430-01A-01 3 0.1824 0.8809 0.004 0.060 0.936 0.000
#> TCGA-06-0125-01A-01 3 0.4920 0.7570 0.164 0.068 0.768 0.000
#> TCGA-06-0126-01A-01 3 0.4875 0.7607 0.160 0.068 0.772 0.000
#> TCGA-06-0137-01A-03 3 0.3548 0.8436 0.068 0.068 0.864 0.000
#> TCGA-06-0145-01A-04 3 0.1902 0.8792 0.004 0.064 0.932 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-06-0187-01A-01 3 0.1489 0.8887 0.004 0.044 0.952 0.000
#> TCGA-06-0211-01B-01 3 0.3400 0.7562 0.000 0.000 0.820 0.180
#> TCGA-06-0402-01A-01 3 0.4949 0.7385 0.180 0.060 0.760 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-08-0354-01A-01 3 0.0895 0.8965 0.000 0.004 0.976 0.020
#> TCGA-08-0355-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-08-0357-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-08-0358-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-08-0375-01A-01 3 0.1824 0.8809 0.004 0.060 0.936 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-08-0518-01A-01 3 0.3081 0.8586 0.048 0.064 0.888 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0057-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0004-01A-01 2 0.2329 0.8470 0.000 0.916 0.012 0.072
#> TCGA-02-0006-01B-01 2 0.5428 0.4867 0.020 0.600 0.380 0.000
#> TCGA-02-0025-01A-01 2 0.3837 0.8132 0.000 0.776 0.224 0.000
#> TCGA-02-0033-01A-01 2 0.2149 0.8886 0.000 0.912 0.088 0.000
#> TCGA-02-0034-01A-01 3 0.4907 0.1732 0.000 0.420 0.580 0.000
#> TCGA-02-0039-01A-01 2 0.3356 0.8542 0.000 0.824 0.176 0.000
#> TCGA-02-0051-01A-01 2 0.2483 0.8752 0.000 0.916 0.052 0.032
#> TCGA-02-0054-01A-01 2 0.3649 0.8319 0.000 0.796 0.204 0.000
#> TCGA-02-0055-01A-01 2 0.2081 0.8355 0.000 0.916 0.000 0.084
#> TCGA-02-0059-01A-01 2 0.2081 0.8355 0.000 0.916 0.000 0.084
#> TCGA-02-0064-01A-01 3 0.2704 0.8472 0.000 0.124 0.876 0.000
#> TCGA-02-0075-01A-01 3 0.6585 0.6211 0.180 0.188 0.632 0.000
#> TCGA-02-0079-01A-03 3 0.0188 0.9028 0.000 0.004 0.996 0.000
#> TCGA-02-0085-01A-01 4 0.6130 0.2076 0.000 0.052 0.400 0.548
#> TCGA-02-0086-01A-01 2 0.4477 0.6945 0.000 0.688 0.312 0.000
#> TCGA-02-0099-01A-01 2 0.1913 0.8710 0.000 0.940 0.040 0.020
#> TCGA-02-0106-01A-01 3 0.0592 0.8981 0.000 0.016 0.984 0.000
#> TCGA-02-0107-01A-01 2 0.2450 0.8491 0.000 0.912 0.016 0.072
#> TCGA-02-0111-01A-01 2 0.3311 0.8555 0.000 0.828 0.172 0.000
#> TCGA-02-0326-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-02-0337-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-06-0122-01A-01 3 0.5007 0.7517 0.172 0.068 0.760 0.000
#> TCGA-06-0124-01A-01 3 0.1576 0.8869 0.004 0.048 0.948 0.000
#> TCGA-06-0130-01A-01 2 0.2149 0.8886 0.000 0.912 0.088 0.000
#> TCGA-06-0139-01A-01 2 0.2149 0.8886 0.000 0.912 0.088 0.000
#> TCGA-06-0143-01A-01 3 0.4782 0.7564 0.152 0.068 0.780 0.000
#> TCGA-06-0147-01A-01 2 0.2149 0.8886 0.000 0.912 0.088 0.000
#> TCGA-06-0149-01A-05 3 0.0336 0.9010 0.000 0.008 0.992 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-06-0154-01A-02 3 0.1867 0.8615 0.000 0.072 0.928 0.000
#> TCGA-06-0164-01A-01 2 0.2149 0.8886 0.000 0.912 0.088 0.000
#> TCGA-06-0175-01A-01 3 0.0817 0.8977 0.024 0.000 0.976 0.000
#> TCGA-06-0176-01A-03 2 0.2530 0.8807 0.000 0.888 0.112 0.000
#> TCGA-06-0184-01A-01 4 0.4040 0.6241 0.000 0.248 0.000 0.752
#> TCGA-06-0189-01A-05 2 0.3528 0.7414 0.000 0.808 0.000 0.192
#> TCGA-06-0190-01A-01 2 0.2149 0.8886 0.000 0.912 0.088 0.000
#> TCGA-06-0194-01A-01 2 0.3356 0.8542 0.000 0.824 0.176 0.000
#> TCGA-06-0197-01A-02 2 0.2081 0.8355 0.000 0.916 0.000 0.084
#> TCGA-06-0210-01A-01 3 0.3873 0.6899 0.000 0.228 0.772 0.000
#> TCGA-06-0397-01A-01 2 0.3160 0.8345 0.020 0.872 0.108 0.000
#> TCGA-06-0409-01A-02 2 0.2149 0.8886 0.000 0.912 0.088 0.000
#> TCGA-06-0412-01A-01 3 0.2345 0.8463 0.000 0.100 0.900 0.000
#> TCGA-06-0644-01A-02 2 0.2081 0.8872 0.000 0.916 0.084 0.000
#> TCGA-06-0645-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-08-0346-01A-01 2 0.3400 0.8517 0.000 0.820 0.180 0.000
#> TCGA-08-0352-01A-01 3 0.0000 0.9038 0.000 0.000 1.000 0.000
#> TCGA-08-0360-01A-01 2 0.3356 0.8542 0.000 0.824 0.176 0.000
#> TCGA-08-0390-01A-01 2 0.5615 0.4880 0.000 0.612 0.032 0.356
#> TCGA-08-0392-01A-01 2 0.3444 0.7638 0.000 0.816 0.000 0.184
#> TCGA-08-0509-01A-01 2 0.2149 0.8886 0.000 0.912 0.088 0.000
#> TCGA-08-0510-01A-01 3 0.4842 0.7527 0.048 0.192 0.760 0.000
#> TCGA-08-0512-01A-01 2 0.1792 0.8826 0.000 0.932 0.068 0.000
#> TCGA-08-0522-01A-01 2 0.2149 0.8886 0.000 0.912 0.088 0.000
#> TCGA-12-0619-01A-01 3 0.3219 0.7942 0.000 0.164 0.836 0.000
#> TCGA-12-0620-01A-01 3 0.4933 0.0278 0.000 0.432 0.568 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.0000 0.8842 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0404 0.8817 0.988 0.000 0.000 0.000 0.012
#> TCGA-02-0011-01B-01 1 0.0000 0.8842 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.8842 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.8842 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0609 0.8795 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0028-01A-01 1 0.0703 0.8787 0.976 0.000 0.000 0.000 0.024
#> TCGA-02-0046-01A-01 1 0.0000 0.8842 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0048-01A-01 1 0.2127 0.8243 0.892 0.000 0.000 0.000 0.108
#> TCGA-02-0060-01A-01 1 0.1671 0.8498 0.924 0.000 0.000 0.076 0.000
#> TCGA-02-0069-01A-01 1 0.3999 0.3878 0.656 0.000 0.000 0.000 0.344
#> TCGA-02-0074-01A-01 1 0.2377 0.7963 0.872 0.000 0.000 0.000 0.128
#> TCGA-02-0080-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0084-01A-03 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0087-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0104-01A-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.8842 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.3558 0.7968 0.828 0.000 0.064 0.000 0.108
#> TCGA-02-0321-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0325-01A-01 5 0.2905 0.9148 0.096 0.000 0.036 0.000 0.868
#> TCGA-02-0338-01A-01 1 0.0000 0.8842 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.1648 0.8693 0.940 0.000 0.040 0.000 0.020
#> TCGA-02-0432-01A-02 1 0.4210 0.7506 0.780 0.000 0.096 0.124 0.000
#> TCGA-02-0439-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0440-01A-01 1 0.0510 0.8814 0.984 0.000 0.016 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.1121 0.8681 0.956 0.000 0.000 0.044 0.000
#> TCGA-06-0128-01A-01 3 0.7150 0.1397 0.356 0.000 0.468 0.088 0.088
#> TCGA-06-0129-01A-01 5 0.2377 0.8695 0.128 0.000 0.000 0.000 0.872
#> TCGA-06-0146-01A-01 1 0.2570 0.8412 0.888 0.000 0.028 0.000 0.084
#> TCGA-06-0156-01A-01 4 0.4999 0.6704 0.148 0.128 0.004 0.720 0.000
#> TCGA-06-0166-01A-01 1 0.5264 0.5904 0.652 0.000 0.092 0.256 0.000
#> TCGA-06-0174-01A-01 1 0.0000 0.8842 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.4219 0.3435 0.584 0.000 0.416 0.000 0.000
#> TCGA-06-0238-01A-02 4 0.0162 0.9255 0.000 0.000 0.004 0.996 0.000
#> TCGA-06-0241-01A-02 1 0.0609 0.8795 0.980 0.000 0.000 0.020 0.000
#> TCGA-06-0410-01A-01 4 0.4045 0.7443 0.136 0.000 0.064 0.796 0.004
#> TCGA-06-0413-01A-01 1 0.0000 0.8842 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.8842 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.0865 0.8941 0.004 0.024 0.972 0.000 0.000
#> TCGA-06-0648-01A-01 1 0.4573 0.5618 0.700 0.000 0.256 0.044 0.000
#> TCGA-08-0245-01A-01 1 0.3056 0.8235 0.864 0.000 0.068 0.000 0.068
#> TCGA-08-0344-01A-01 1 0.3730 0.6223 0.712 0.000 0.000 0.288 0.000
#> TCGA-08-0347-01A-01 3 0.0290 0.9028 0.000 0.000 0.992 0.008 0.000
#> TCGA-08-0348-01A-01 1 0.1478 0.8525 0.936 0.000 0.064 0.000 0.000
#> TCGA-08-0350-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0353-01A-01 3 0.3427 0.7947 0.056 0.000 0.836 0.000 0.108
#> TCGA-08-0359-01A-01 1 0.1956 0.8503 0.916 0.000 0.008 0.076 0.000
#> TCGA-08-0385-01A-01 3 0.6050 0.2452 0.128 0.000 0.512 0.360 0.000
#> TCGA-08-0517-01A-01 1 0.1579 0.8739 0.944 0.000 0.024 0.000 0.032
#> TCGA-08-0524-01A-01 1 0.1571 0.8552 0.936 0.000 0.060 0.004 0.000
#> TCGA-12-0616-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.8842 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0113-01A-01 3 0.4874 0.3932 0.000 0.000 0.600 0.368 0.032
#> TCGA-02-0115-01A-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0451-01A-01 4 0.1012 0.9077 0.012 0.000 0.020 0.968 0.000
#> TCGA-06-0132-01A-02 4 0.3460 0.8261 0.000 0.044 0.000 0.828 0.128
#> TCGA-06-0133-01A-02 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0138-01A-02 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0160-01A-01 4 0.3460 0.8261 0.000 0.044 0.000 0.828 0.128
#> TCGA-06-0162-01A-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0167-01A-01 4 0.3460 0.8261 0.000 0.044 0.000 0.828 0.128
#> TCGA-06-0171-01A-02 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0173-01A-01 4 0.0898 0.9121 0.020 0.000 0.008 0.972 0.000
#> TCGA-06-0179-01A-02 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0182-01A-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0185-01A-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0195-01B-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0208-01B-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0214-01A-02 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0219-01A-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0221-01A-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0237-01A-02 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0240-01A-02 4 0.3460 0.8261 0.000 0.044 0.000 0.828 0.128
#> TCGA-08-0349-01A-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-08-0380-01A-01 2 0.3636 0.6580 0.000 0.728 0.000 0.272 0.000
#> TCGA-08-0386-01A-01 3 0.4443 0.7661 0.048 0.000 0.800 0.084 0.068
#> TCGA-08-0520-01A-01 4 0.0000 0.9285 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0007-01A-01 3 0.4471 0.7172 0.120 0.000 0.768 0.004 0.108
#> TCGA-02-0009-01A-01 5 0.2928 0.9488 0.064 0.000 0.064 0.000 0.872
#> TCGA-02-0016-01A-01 3 0.1544 0.8691 0.000 0.000 0.932 0.000 0.068
#> TCGA-02-0021-01A-01 3 0.3039 0.7555 0.000 0.000 0.808 0.000 0.192
#> TCGA-02-0023-01B-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0027-01A-01 1 0.2677 0.8144 0.872 0.000 0.016 0.000 0.112
#> TCGA-02-0038-01A-01 3 0.1410 0.8749 0.000 0.000 0.940 0.000 0.060
#> TCGA-02-0043-01A-01 5 0.2928 0.9488 0.064 0.000 0.064 0.000 0.872
#> TCGA-02-0070-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0102-01A-01 5 0.2928 0.9488 0.064 0.000 0.064 0.000 0.872
#> TCGA-02-0260-01A-03 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.2127 0.8362 0.000 0.000 0.892 0.000 0.108
#> TCGA-06-0125-01A-01 5 0.2928 0.9488 0.064 0.000 0.064 0.000 0.872
#> TCGA-06-0126-01A-01 5 0.2928 0.9488 0.064 0.000 0.064 0.000 0.872
#> TCGA-06-0137-01A-03 5 0.3033 0.9391 0.052 0.000 0.084 0.000 0.864
#> TCGA-06-0145-01A-04 5 0.2471 0.8847 0.000 0.000 0.136 0.000 0.864
#> TCGA-06-0148-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0187-01A-01 3 0.1792 0.8573 0.000 0.000 0.916 0.000 0.084
#> TCGA-06-0211-01B-01 3 0.2929 0.7316 0.000 0.000 0.820 0.180 0.000
#> TCGA-06-0402-01A-01 3 0.4450 0.6988 0.132 0.000 0.760 0.000 0.108
#> TCGA-08-0246-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0354-01A-01 3 0.0898 0.8943 0.000 0.008 0.972 0.020 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0357-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0358-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0375-01A-01 3 0.2127 0.8362 0.000 0.000 0.892 0.000 0.108
#> TCGA-08-0511-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0518-01A-01 5 0.3283 0.8844 0.028 0.000 0.140 0.000 0.832
#> TCGA-08-0529-01A-02 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0057-01A-01 3 0.0703 0.8960 0.000 0.000 0.976 0.000 0.024
#> TCGA-02-0004-01A-01 2 0.1251 0.8808 0.000 0.956 0.008 0.036 0.000
#> TCGA-02-0006-01B-01 2 0.4416 0.4833 0.012 0.632 0.356 0.000 0.000
#> TCGA-02-0025-01A-01 2 0.2732 0.8234 0.000 0.840 0.160 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.1270 0.9021 0.000 0.948 0.052 0.000 0.000
#> TCGA-02-0034-01A-01 3 0.4171 0.3050 0.000 0.396 0.604 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.2127 0.8774 0.000 0.892 0.108 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.1300 0.8937 0.000 0.956 0.028 0.016 0.000
#> TCGA-02-0054-01A-01 2 0.2773 0.8218 0.000 0.836 0.164 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.1121 0.8741 0.000 0.956 0.000 0.044 0.000
#> TCGA-02-0059-01A-01 2 0.1121 0.8741 0.000 0.956 0.000 0.044 0.000
#> TCGA-02-0064-01A-01 3 0.3033 0.8300 0.000 0.084 0.864 0.000 0.052
#> TCGA-02-0075-01A-01 5 0.3844 0.9008 0.064 0.068 0.032 0.000 0.836
#> TCGA-02-0079-01A-03 3 0.0290 0.9023 0.000 0.008 0.992 0.000 0.000
#> TCGA-02-0085-01A-01 4 0.4808 0.2619 0.000 0.024 0.400 0.576 0.000
#> TCGA-02-0086-01A-01 2 0.3684 0.6724 0.000 0.720 0.280 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.1588 0.8930 0.000 0.948 0.028 0.008 0.016
#> TCGA-02-0106-01A-01 3 0.0404 0.9016 0.000 0.012 0.988 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.1444 0.8830 0.000 0.948 0.012 0.040 0.000
#> TCGA-02-0111-01A-01 2 0.1965 0.8822 0.000 0.904 0.096 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0337-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0122-01A-01 5 0.2903 0.9360 0.080 0.000 0.048 0.000 0.872
#> TCGA-06-0124-01A-01 3 0.2230 0.8362 0.000 0.000 0.884 0.000 0.116
#> TCGA-06-0130-01A-01 2 0.1270 0.9021 0.000 0.948 0.052 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.1270 0.9021 0.000 0.948 0.052 0.000 0.000
#> TCGA-06-0143-01A-01 5 0.2761 0.9180 0.024 0.000 0.104 0.000 0.872
#> TCGA-06-0147-01A-01 2 0.1270 0.9021 0.000 0.948 0.052 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.0290 0.9030 0.000 0.008 0.992 0.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0154-01A-02 3 0.1121 0.8799 0.000 0.044 0.956 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.1270 0.9021 0.000 0.948 0.052 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.0703 0.8960 0.024 0.000 0.976 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.1671 0.8919 0.000 0.924 0.076 0.000 0.000
#> TCGA-06-0184-01A-01 4 0.3366 0.6551 0.000 0.232 0.000 0.768 0.000
#> TCGA-06-0189-01A-05 2 0.3003 0.7553 0.000 0.812 0.000 0.188 0.000
#> TCGA-06-0190-01A-01 2 0.1270 0.9021 0.000 0.948 0.052 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.2074 0.8794 0.000 0.896 0.104 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.1121 0.8741 0.000 0.956 0.000 0.044 0.000
#> TCGA-06-0210-01A-01 3 0.3395 0.6918 0.000 0.236 0.764 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.3009 0.8558 0.008 0.876 0.064 0.000 0.052
#> TCGA-06-0409-01A-02 2 0.1270 0.9021 0.000 0.948 0.052 0.000 0.000
#> TCGA-06-0412-01A-01 3 0.2513 0.8226 0.000 0.116 0.876 0.000 0.008
#> TCGA-06-0644-01A-02 2 0.1121 0.8990 0.000 0.956 0.044 0.000 0.000
#> TCGA-06-0645-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.2179 0.8738 0.000 0.888 0.112 0.000 0.000
#> TCGA-08-0352-01A-01 3 0.0000 0.9061 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0360-01A-01 2 0.2074 0.8794 0.000 0.896 0.104 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.4794 0.5035 0.000 0.624 0.032 0.344 0.000
#> TCGA-08-0392-01A-01 2 0.2329 0.8269 0.000 0.876 0.000 0.124 0.000
#> TCGA-08-0509-01A-01 2 0.1270 0.9021 0.000 0.948 0.052 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.5367 0.6752 0.032 0.132 0.720 0.000 0.116
#> TCGA-08-0512-01A-01 2 0.1444 0.8976 0.000 0.948 0.040 0.000 0.012
#> TCGA-08-0522-01A-01 2 0.1270 0.9021 0.000 0.948 0.052 0.000 0.000
#> TCGA-12-0619-01A-01 3 0.2825 0.8146 0.000 0.124 0.860 0.000 0.016
#> TCGA-12-0620-01A-01 3 0.4268 0.0666 0.000 0.444 0.556 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.0363 0.888 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-02-0010-01A-01 1 0.0790 0.884 0.968 0.000 0.000 0.000 0.032 0.000
#> TCGA-02-0011-01B-01 1 0.0363 0.888 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-02-0014-01A-01 1 0.0363 0.888 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.885 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0937 0.882 0.960 0.000 0.000 0.000 0.040 0.000
#> TCGA-02-0028-01A-01 1 0.1007 0.881 0.956 0.000 0.000 0.000 0.044 0.000
#> TCGA-02-0046-01A-01 1 0.0363 0.888 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-02-0047-01A-01 6 0.0508 0.918 0.012 0.000 0.000 0.000 0.004 0.984
#> TCGA-02-0048-01A-01 1 0.2527 0.793 0.832 0.000 0.000 0.000 0.168 0.000
#> TCGA-02-0060-01A-01 1 0.2051 0.823 0.896 0.000 0.004 0.000 0.004 0.096
#> TCGA-02-0069-01A-01 1 0.3659 0.426 0.636 0.000 0.000 0.000 0.364 0.000
#> TCGA-02-0074-01A-01 1 0.2340 0.801 0.852 0.000 0.000 0.000 0.148 0.000
#> TCGA-02-0080-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0084-01A-03 3 0.0146 0.898 0.004 0.000 0.996 0.000 0.000 0.000
#> TCGA-02-0087-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0104-01A-01 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-02-0114-01A-01 1 0.0363 0.888 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-02-0281-01A-01 1 0.2859 0.789 0.828 0.000 0.016 0.000 0.156 0.000
#> TCGA-02-0321-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0325-01A-01 5 0.0260 0.972 0.008 0.000 0.000 0.000 0.992 0.000
#> TCGA-02-0338-01A-01 1 0.0363 0.888 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-02-0339-01A-01 1 0.0972 0.881 0.964 0.000 0.008 0.000 0.028 0.000
#> TCGA-02-0432-01A-02 1 0.3605 0.749 0.804 0.000 0.084 0.000 0.004 0.108
#> TCGA-02-0439-01A-01 3 0.0405 0.897 0.008 0.000 0.988 0.000 0.004 0.000
#> TCGA-02-0440-01A-01 1 0.0146 0.887 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0446-01A-01 1 0.0291 0.884 0.992 0.000 0.000 0.000 0.004 0.004
#> TCGA-06-0128-01A-01 3 0.6696 0.233 0.300 0.000 0.476 0.000 0.136 0.088
#> TCGA-06-0129-01A-01 5 0.0146 0.975 0.004 0.000 0.000 0.000 0.996 0.000
#> TCGA-06-0146-01A-01 1 0.2491 0.829 0.868 0.000 0.020 0.000 0.112 0.000
#> TCGA-06-0156-01A-01 6 0.4566 0.556 0.140 0.160 0.000 0.000 0.000 0.700
#> TCGA-06-0166-01A-01 1 0.4707 0.556 0.656 0.000 0.092 0.000 0.000 0.252
#> TCGA-06-0174-01A-01 1 0.0363 0.888 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-06-0177-01A-01 1 0.3765 0.337 0.596 0.000 0.404 0.000 0.000 0.000
#> TCGA-06-0238-01A-02 6 0.0146 0.925 0.000 0.000 0.004 0.000 0.000 0.996
#> TCGA-06-0241-01A-02 1 0.0405 0.887 0.988 0.000 0.000 0.000 0.008 0.004
#> TCGA-06-0410-01A-01 6 0.3785 0.671 0.152 0.000 0.064 0.000 0.004 0.780
#> TCGA-06-0413-01A-01 1 0.0363 0.888 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-06-0414-01A-01 1 0.0363 0.888 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-06-0646-01A-01 3 0.0777 0.892 0.004 0.024 0.972 0.000 0.000 0.000
#> TCGA-06-0648-01A-01 1 0.3780 0.582 0.744 0.000 0.224 0.000 0.004 0.028
#> TCGA-08-0245-01A-01 1 0.2445 0.827 0.872 0.000 0.020 0.000 0.108 0.000
#> TCGA-08-0344-01A-01 1 0.3290 0.631 0.744 0.000 0.000 0.000 0.004 0.252
#> TCGA-08-0347-01A-01 3 0.0767 0.893 0.012 0.000 0.976 0.000 0.004 0.008
#> TCGA-08-0348-01A-01 1 0.0146 0.884 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-08-0350-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0353-01A-01 3 0.3445 0.773 0.048 0.000 0.796 0.000 0.156 0.000
#> TCGA-08-0359-01A-01 1 0.0858 0.874 0.968 0.000 0.000 0.000 0.004 0.028
#> TCGA-08-0385-01A-01 3 0.5434 0.252 0.128 0.000 0.512 0.000 0.000 0.360
#> TCGA-08-0517-01A-01 1 0.1398 0.874 0.940 0.000 0.008 0.000 0.052 0.000
#> TCGA-08-0524-01A-01 1 0.0260 0.884 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0363 0.888 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-02-0089-01A-01 6 0.0146 0.926 0.004 0.000 0.000 0.000 0.000 0.996
#> TCGA-02-0113-01A-01 3 0.4563 0.381 0.000 0.000 0.588 0.000 0.044 0.368
#> TCGA-02-0115-01A-01 6 0.0508 0.918 0.012 0.000 0.000 0.000 0.004 0.984
#> TCGA-02-0451-01A-01 6 0.1148 0.897 0.016 0.000 0.020 0.000 0.004 0.960
#> TCGA-06-0132-01A-02 4 0.0713 0.963 0.000 0.000 0.000 0.972 0.000 0.028
#> TCGA-06-0133-01A-02 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0162-01A-01 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0171-01A-02 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 6 0.0972 0.899 0.028 0.000 0.008 0.000 0.000 0.964
#> TCGA-06-0179-01A-02 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0195-01B-01 6 0.0146 0.926 0.000 0.000 0.000 0.004 0.000 0.996
#> TCGA-06-0208-01B-01 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.0000 0.988 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0349-01A-01 6 0.0146 0.926 0.004 0.000 0.000 0.000 0.000 0.996
#> TCGA-08-0380-01A-01 2 0.3198 0.638 0.000 0.740 0.000 0.000 0.000 0.260
#> TCGA-08-0386-01A-01 3 0.3999 0.784 0.048 0.000 0.796 0.000 0.104 0.052
#> TCGA-08-0520-01A-01 6 0.0000 0.928 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.4270 0.713 0.100 0.000 0.740 0.000 0.156 0.004
#> TCGA-02-0009-01A-01 5 0.0146 0.975 0.004 0.000 0.000 0.000 0.996 0.000
#> TCGA-02-0016-01A-01 3 0.1863 0.849 0.000 0.000 0.896 0.000 0.104 0.000
#> TCGA-02-0021-01A-01 3 0.3076 0.725 0.000 0.000 0.760 0.000 0.240 0.000
#> TCGA-02-0023-01B-01 3 0.0508 0.895 0.012 0.000 0.984 0.000 0.004 0.000
#> TCGA-02-0027-01A-01 1 0.2981 0.789 0.820 0.000 0.020 0.000 0.160 0.000
#> TCGA-02-0038-01A-01 3 0.1765 0.854 0.000 0.000 0.904 0.000 0.096 0.000
#> TCGA-02-0043-01A-01 5 0.0146 0.975 0.004 0.000 0.000 0.000 0.996 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0102-01A-01 5 0.0146 0.975 0.004 0.000 0.000 0.000 0.996 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.2416 0.808 0.000 0.000 0.844 0.000 0.156 0.000
#> TCGA-06-0125-01A-01 5 0.0146 0.975 0.004 0.000 0.000 0.000 0.996 0.000
#> TCGA-06-0126-01A-01 5 0.0146 0.975 0.004 0.000 0.000 0.000 0.996 0.000
#> TCGA-06-0137-01A-03 5 0.0603 0.963 0.004 0.000 0.016 0.000 0.980 0.000
#> TCGA-06-0145-01A-04 5 0.0865 0.934 0.000 0.000 0.036 0.000 0.964 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0187-01A-01 3 0.2092 0.835 0.000 0.000 0.876 0.000 0.124 0.000
#> TCGA-06-0211-01B-01 3 0.2631 0.734 0.000 0.000 0.820 0.000 0.000 0.180
#> TCGA-06-0402-01A-01 3 0.3894 0.737 0.072 0.000 0.760 0.000 0.168 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0354-01A-01 3 0.1092 0.886 0.000 0.020 0.960 0.000 0.000 0.020
#> TCGA-08-0355-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0357-01A-01 3 0.0508 0.895 0.012 0.000 0.984 0.000 0.004 0.000
#> TCGA-08-0358-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0375-01A-01 3 0.2416 0.808 0.000 0.000 0.844 0.000 0.156 0.000
#> TCGA-08-0511-01A-01 3 0.0508 0.895 0.012 0.000 0.984 0.000 0.004 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0518-01A-01 5 0.1349 0.900 0.004 0.000 0.056 0.000 0.940 0.000
#> TCGA-08-0529-01A-02 3 0.0146 0.899 0.000 0.000 0.996 0.000 0.004 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0057-01A-01 3 0.0713 0.890 0.000 0.000 0.972 0.000 0.028 0.000
#> TCGA-02-0004-01A-01 2 0.0000 0.897 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.3714 0.449 0.000 0.656 0.340 0.000 0.004 0.000
#> TCGA-02-0025-01A-01 2 0.2178 0.801 0.000 0.868 0.132 0.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0547 0.906 0.000 0.980 0.020 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 3 0.3737 0.346 0.000 0.392 0.608 0.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.1707 0.884 0.012 0.928 0.056 0.000 0.004 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.897 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.2300 0.796 0.000 0.856 0.144 0.000 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.897 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.897 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0064-01A-01 3 0.2794 0.832 0.000 0.080 0.860 0.000 0.060 0.000
#> TCGA-02-0075-01A-01 5 0.1155 0.938 0.004 0.036 0.004 0.000 0.956 0.000
#> TCGA-02-0079-01A-03 3 0.0547 0.893 0.000 0.020 0.980 0.000 0.000 0.000
#> TCGA-02-0085-01A-01 6 0.4545 0.240 0.012 0.012 0.400 0.000 0.004 0.572
#> TCGA-02-0086-01A-01 2 0.3309 0.605 0.000 0.720 0.280 0.000 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.0603 0.905 0.000 0.980 0.016 0.000 0.004 0.000
#> TCGA-02-0106-01A-01 3 0.0363 0.897 0.000 0.012 0.988 0.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0603 0.898 0.000 0.980 0.004 0.000 0.000 0.016
#> TCGA-02-0111-01A-01 2 0.0865 0.892 0.000 0.964 0.036 0.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0337-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0122-01A-01 5 0.0146 0.975 0.004 0.000 0.000 0.000 0.996 0.000
#> TCGA-06-0124-01A-01 3 0.2416 0.815 0.000 0.000 0.844 0.000 0.156 0.000
#> TCGA-06-0130-01A-01 2 0.0547 0.906 0.000 0.980 0.020 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0547 0.906 0.000 0.980 0.020 0.000 0.000 0.000
#> TCGA-06-0143-01A-01 5 0.0363 0.964 0.000 0.000 0.012 0.000 0.988 0.000
#> TCGA-06-0147-01A-01 2 0.0547 0.906 0.000 0.980 0.020 0.000 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.0260 0.898 0.000 0.008 0.992 0.000 0.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0154-01A-02 3 0.0790 0.885 0.000 0.032 0.968 0.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0547 0.906 0.000 0.980 0.020 0.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.0632 0.892 0.024 0.000 0.976 0.000 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.1007 0.893 0.000 0.956 0.044 0.000 0.000 0.000
#> TCGA-06-0184-01A-01 6 0.2996 0.610 0.000 0.228 0.000 0.000 0.000 0.772
#> TCGA-06-0189-01A-05 2 0.2631 0.725 0.000 0.820 0.000 0.000 0.000 0.180
#> TCGA-06-0190-01A-01 2 0.0547 0.906 0.000 0.980 0.020 0.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.1204 0.889 0.000 0.944 0.056 0.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.897 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0210-01A-01 3 0.3126 0.685 0.000 0.248 0.752 0.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.2007 0.873 0.004 0.916 0.044 0.000 0.036 0.000
#> TCGA-06-0409-01A-02 2 0.0547 0.906 0.000 0.980 0.020 0.000 0.000 0.000
#> TCGA-06-0412-01A-01 3 0.2431 0.812 0.000 0.132 0.860 0.000 0.008 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.897 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0645-01A-01 3 0.0000 0.900 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.1387 0.882 0.000 0.932 0.068 0.000 0.000 0.000
#> TCGA-08-0352-01A-01 3 0.0508 0.895 0.012 0.000 0.984 0.000 0.004 0.000
#> TCGA-08-0360-01A-01 2 0.1204 0.889 0.000 0.944 0.056 0.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.4649 0.487 0.012 0.628 0.028 0.000 0.004 0.328
#> TCGA-08-0392-01A-01 2 0.1714 0.836 0.000 0.908 0.000 0.000 0.000 0.092
#> TCGA-08-0509-01A-01 2 0.0547 0.906 0.000 0.980 0.020 0.000 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.5118 0.653 0.028 0.132 0.684 0.000 0.156 0.000
#> TCGA-08-0512-01A-01 2 0.0603 0.905 0.000 0.980 0.016 0.000 0.004 0.000
#> TCGA-08-0522-01A-01 2 0.0547 0.906 0.000 0.980 0.020 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 3 0.2312 0.831 0.000 0.112 0.876 0.000 0.012 0.000
#> TCGA-12-0620-01A-01 3 0.3833 0.110 0.000 0.444 0.556 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> CV:pam 171 1.79e-20 2
#> CV:pam 157 5.09e-37 3
#> CV:pam 162 7.74e-53 4
#> CV:pam 164 2.78e-50 5
#> CV:pam 163 4.18e-48 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "mclust"]
# you can also extract it by
# res = res_list["CV:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.320 0.758 0.857 0.210 0.922 0.922
#> 3 3 0.192 0.595 0.765 1.416 0.531 0.493
#> 4 4 0.423 0.632 0.800 0.266 0.858 0.710
#> 5 5 0.431 0.542 0.727 0.139 0.773 0.472
#> 6 6 0.514 0.577 0.732 0.063 0.924 0.720
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 2 0.563 0.791 0.132 0.868
#> TCGA-02-0010-01A-01 2 0.482 0.802 0.104 0.896
#> TCGA-02-0011-01B-01 2 0.388 0.813 0.076 0.924
#> TCGA-02-0014-01A-01 2 0.529 0.799 0.120 0.880
#> TCGA-02-0024-01B-01 2 0.552 0.796 0.128 0.872
#> TCGA-02-0026-01B-01 2 0.443 0.810 0.092 0.908
#> TCGA-02-0028-01A-01 2 0.430 0.807 0.088 0.912
#> TCGA-02-0046-01A-01 2 0.518 0.800 0.116 0.884
#> TCGA-02-0047-01A-01 2 0.767 0.608 0.224 0.776
#> TCGA-02-0048-01A-01 2 0.494 0.805 0.108 0.892
#> TCGA-02-0060-01A-01 2 0.469 0.806 0.100 0.900
#> TCGA-02-0069-01A-01 2 0.443 0.807 0.092 0.908
#> TCGA-02-0074-01A-01 2 0.443 0.810 0.092 0.908
#> TCGA-02-0080-01A-01 2 0.204 0.831 0.032 0.968
#> TCGA-02-0084-01A-03 2 0.118 0.832 0.016 0.984
#> TCGA-02-0087-01A-01 2 0.118 0.832 0.016 0.984
#> TCGA-02-0104-01A-01 2 0.482 0.807 0.104 0.896
#> TCGA-02-0114-01A-01 2 0.506 0.801 0.112 0.888
#> TCGA-02-0281-01A-01 2 0.456 0.817 0.096 0.904
#> TCGA-02-0321-01A-01 2 0.311 0.822 0.056 0.944
#> TCGA-02-0325-01A-01 2 0.204 0.831 0.032 0.968
#> TCGA-02-0338-01A-01 2 0.518 0.800 0.116 0.884
#> TCGA-02-0339-01A-01 2 0.402 0.812 0.080 0.920
#> TCGA-02-0432-01A-02 2 0.184 0.832 0.028 0.972
#> TCGA-02-0439-01A-01 2 0.118 0.832 0.016 0.984
#> TCGA-02-0440-01A-01 2 0.518 0.800 0.116 0.884
#> TCGA-02-0446-01A-01 2 0.730 0.649 0.204 0.796
#> TCGA-06-0128-01A-01 2 0.388 0.818 0.076 0.924
#> TCGA-06-0129-01A-01 2 0.242 0.830 0.040 0.960
#> TCGA-06-0146-01A-01 2 0.204 0.831 0.032 0.968
#> TCGA-06-0156-01A-01 2 0.402 0.813 0.080 0.920
#> TCGA-06-0166-01A-01 2 0.430 0.811 0.088 0.912
#> TCGA-06-0174-01A-01 2 0.518 0.800 0.116 0.884
#> TCGA-06-0177-01A-01 2 0.373 0.816 0.072 0.928
#> TCGA-06-0238-01A-02 2 0.430 0.813 0.088 0.912
#> TCGA-06-0241-01A-02 2 0.494 0.805 0.108 0.892
#> TCGA-06-0410-01A-01 2 0.430 0.812 0.088 0.912
#> TCGA-06-0413-01A-01 2 0.529 0.799 0.120 0.880
#> TCGA-06-0414-01A-01 2 0.518 0.800 0.116 0.884
#> TCGA-06-0646-01A-01 2 0.224 0.828 0.036 0.964
#> TCGA-06-0648-01A-01 2 0.430 0.813 0.088 0.912
#> TCGA-08-0245-01A-01 2 0.469 0.809 0.100 0.900
#> TCGA-08-0344-01A-01 2 0.456 0.809 0.096 0.904
#> TCGA-08-0347-01A-01 2 0.416 0.813 0.084 0.916
#> TCGA-08-0348-01A-01 2 0.388 0.815 0.076 0.924
#> TCGA-08-0350-01A-01 2 0.118 0.832 0.016 0.984
#> TCGA-08-0353-01A-01 2 0.358 0.818 0.068 0.932
#> TCGA-08-0359-01A-01 2 0.767 0.608 0.224 0.776
#> TCGA-08-0385-01A-01 2 0.358 0.824 0.068 0.932
#> TCGA-08-0517-01A-01 2 0.518 0.800 0.116 0.884
#> TCGA-08-0524-01A-01 2 0.529 0.800 0.120 0.880
#> TCGA-12-0616-01A-01 2 0.402 0.820 0.080 0.920
#> TCGA-12-0618-01A-01 2 0.518 0.801 0.116 0.884
#> TCGA-02-0089-01A-01 2 0.855 0.516 0.280 0.720
#> TCGA-02-0113-01A-01 2 0.506 0.824 0.112 0.888
#> TCGA-02-0115-01A-01 1 0.955 0.957 0.624 0.376
#> TCGA-02-0451-01A-01 2 0.788 0.636 0.236 0.764
#> TCGA-06-0132-01A-02 1 0.943 0.964 0.640 0.360
#> TCGA-06-0133-01A-02 1 0.961 0.940 0.616 0.384
#> TCGA-06-0138-01A-02 2 0.482 0.805 0.104 0.896
#> TCGA-06-0160-01A-01 1 0.925 0.960 0.660 0.340
#> TCGA-06-0162-01A-01 2 0.767 0.608 0.224 0.776
#> TCGA-06-0167-01A-01 1 0.925 0.960 0.660 0.340
#> TCGA-06-0171-01A-02 2 0.671 0.710 0.176 0.824
#> TCGA-06-0173-01A-01 2 0.482 0.802 0.104 0.896
#> TCGA-06-0179-01A-02 1 0.952 0.959 0.628 0.372
#> TCGA-06-0182-01A-01 2 0.443 0.816 0.092 0.908
#> TCGA-06-0185-01A-01 2 0.456 0.801 0.096 0.904
#> TCGA-06-0195-01B-01 2 1.000 -0.619 0.496 0.504
#> TCGA-06-0208-01B-01 2 0.929 0.151 0.344 0.656
#> TCGA-06-0214-01A-02 2 0.506 0.802 0.112 0.888
#> TCGA-06-0219-01A-01 2 0.730 0.654 0.204 0.796
#> TCGA-06-0221-01A-01 2 0.808 0.548 0.248 0.752
#> TCGA-06-0237-01A-02 2 0.469 0.794 0.100 0.900
#> TCGA-06-0240-01A-02 1 0.925 0.960 0.660 0.340
#> TCGA-08-0349-01A-01 2 0.662 0.694 0.172 0.828
#> TCGA-08-0380-01A-01 2 0.388 0.794 0.076 0.924
#> TCGA-08-0386-01A-01 2 0.402 0.813 0.080 0.920
#> TCGA-08-0520-01A-01 2 0.327 0.816 0.060 0.940
#> TCGA-02-0007-01A-01 2 0.163 0.835 0.024 0.976
#> TCGA-02-0009-01A-01 2 0.358 0.824 0.068 0.932
#> TCGA-02-0016-01A-01 2 0.141 0.832 0.020 0.980
#> TCGA-02-0021-01A-01 2 0.343 0.828 0.064 0.936
#> TCGA-02-0023-01B-01 2 0.118 0.832 0.016 0.984
#> TCGA-02-0027-01A-01 2 0.311 0.829 0.056 0.944
#> TCGA-02-0038-01A-01 2 0.430 0.829 0.088 0.912
#> TCGA-02-0043-01A-01 2 0.327 0.834 0.060 0.940
#> TCGA-02-0070-01A-01 2 0.295 0.825 0.052 0.948
#> TCGA-02-0102-01A-01 2 0.373 0.831 0.072 0.928
#> TCGA-02-0260-01A-03 2 0.204 0.831 0.032 0.968
#> TCGA-02-0269-01B-01 2 0.118 0.832 0.016 0.984
#> TCGA-02-0285-01A-01 2 0.204 0.832 0.032 0.968
#> TCGA-02-0289-01A-01 2 0.204 0.831 0.032 0.968
#> TCGA-02-0290-01A-01 2 0.242 0.829 0.040 0.960
#> TCGA-02-0317-01A-01 2 0.118 0.832 0.016 0.984
#> TCGA-02-0333-01A-02 2 0.118 0.832 0.016 0.984
#> TCGA-02-0422-01A-01 2 0.278 0.826 0.048 0.952
#> TCGA-02-0430-01A-01 2 0.184 0.833 0.028 0.972
#> TCGA-06-0125-01A-01 2 0.327 0.830 0.060 0.940
#> TCGA-06-0126-01A-01 2 0.311 0.829 0.056 0.944
#> TCGA-06-0137-01A-03 2 0.260 0.834 0.044 0.956
#> TCGA-06-0145-01A-04 2 0.311 0.826 0.056 0.944
#> TCGA-06-0148-01A-01 2 0.311 0.823 0.056 0.944
#> TCGA-06-0187-01A-01 2 0.224 0.830 0.036 0.964
#> TCGA-06-0211-01B-01 2 0.430 0.811 0.088 0.912
#> TCGA-06-0402-01A-01 2 0.456 0.831 0.096 0.904
#> TCGA-08-0246-01A-01 2 0.327 0.821 0.060 0.940
#> TCGA-08-0354-01A-01 2 0.278 0.829 0.048 0.952
#> TCGA-08-0355-01A-01 2 0.118 0.832 0.016 0.984
#> TCGA-08-0357-01A-01 2 0.118 0.833 0.016 0.984
#> TCGA-08-0358-01A-01 2 0.141 0.833 0.020 0.980
#> TCGA-08-0375-01A-01 2 0.204 0.831 0.032 0.968
#> TCGA-08-0511-01A-01 2 0.327 0.833 0.060 0.940
#> TCGA-08-0514-01A-01 2 0.311 0.823 0.056 0.944
#> TCGA-08-0518-01A-01 2 0.327 0.829 0.060 0.940
#> TCGA-08-0529-01A-02 2 0.295 0.824 0.052 0.948
#> TCGA-08-0531-01A-01 2 0.295 0.824 0.052 0.948
#> TCGA-02-0057-01A-01 2 0.358 0.824 0.068 0.932
#> TCGA-02-0004-01A-01 2 0.917 0.497 0.332 0.668
#> TCGA-02-0006-01B-01 2 0.541 0.826 0.124 0.876
#> TCGA-02-0025-01A-01 2 0.278 0.826 0.048 0.952
#> TCGA-02-0033-01A-01 2 0.917 0.497 0.332 0.668
#> TCGA-02-0034-01A-01 2 0.913 0.502 0.328 0.672
#> TCGA-02-0039-01A-01 2 0.781 0.619 0.232 0.768
#> TCGA-02-0051-01A-01 2 0.402 0.820 0.080 0.920
#> TCGA-02-0054-01A-01 2 0.506 0.829 0.112 0.888
#> TCGA-02-0055-01A-01 2 0.529 0.797 0.120 0.880
#> TCGA-02-0059-01A-01 2 0.402 0.819 0.080 0.920
#> TCGA-02-0064-01A-01 2 0.388 0.832 0.076 0.924
#> TCGA-02-0075-01A-01 2 0.388 0.831 0.076 0.924
#> TCGA-02-0079-01A-03 2 0.118 0.832 0.016 0.984
#> TCGA-02-0085-01A-01 2 0.900 0.407 0.316 0.684
#> TCGA-02-0086-01A-01 2 0.775 0.668 0.228 0.772
#> TCGA-02-0099-01A-01 2 0.482 0.819 0.104 0.896
#> TCGA-02-0106-01A-01 2 0.917 0.497 0.332 0.668
#> TCGA-02-0107-01A-01 2 0.595 0.782 0.144 0.856
#> TCGA-02-0111-01A-01 2 0.518 0.801 0.116 0.884
#> TCGA-02-0326-01A-01 2 0.118 0.832 0.016 0.984
#> TCGA-02-0337-01A-01 2 0.311 0.823 0.056 0.944
#> TCGA-06-0122-01A-01 2 0.311 0.833 0.056 0.944
#> TCGA-06-0124-01A-01 2 0.295 0.832 0.052 0.948
#> TCGA-06-0130-01A-01 2 0.917 0.497 0.332 0.668
#> TCGA-06-0139-01A-01 2 0.917 0.497 0.332 0.668
#> TCGA-06-0143-01A-01 2 0.327 0.833 0.060 0.940
#> TCGA-06-0147-01A-01 2 0.876 0.558 0.296 0.704
#> TCGA-06-0149-01A-05 2 0.839 0.562 0.268 0.732
#> TCGA-06-0152-01A-02 2 0.141 0.832 0.020 0.980
#> TCGA-06-0154-01A-02 2 0.909 0.506 0.324 0.676
#> TCGA-06-0164-01A-01 2 0.802 0.644 0.244 0.756
#> TCGA-06-0175-01A-01 2 0.506 0.823 0.112 0.888
#> TCGA-06-0176-01A-03 2 0.917 0.497 0.332 0.668
#> TCGA-06-0184-01A-01 2 0.358 0.829 0.068 0.932
#> TCGA-06-0189-01A-05 2 0.402 0.819 0.080 0.920
#> TCGA-06-0190-01A-01 2 0.917 0.497 0.332 0.668
#> TCGA-06-0194-01A-01 2 0.917 0.497 0.332 0.668
#> TCGA-06-0197-01A-02 2 0.518 0.801 0.116 0.884
#> TCGA-06-0210-01A-01 2 0.913 0.504 0.328 0.672
#> TCGA-06-0397-01A-01 2 0.373 0.826 0.072 0.928
#> TCGA-06-0409-01A-02 2 0.909 0.506 0.324 0.676
#> TCGA-06-0412-01A-01 2 0.891 0.516 0.308 0.692
#> TCGA-06-0644-01A-02 2 0.917 0.497 0.332 0.668
#> TCGA-06-0645-01A-01 2 0.850 0.547 0.276 0.724
#> TCGA-08-0346-01A-01 2 0.881 0.514 0.300 0.700
#> TCGA-08-0352-01A-01 2 0.311 0.827 0.056 0.944
#> TCGA-08-0360-01A-01 2 0.900 0.508 0.316 0.684
#> TCGA-08-0390-01A-01 2 0.373 0.818 0.072 0.928
#> TCGA-08-0392-01A-01 2 0.278 0.833 0.048 0.952
#> TCGA-08-0509-01A-01 2 0.788 0.635 0.236 0.764
#> TCGA-08-0510-01A-01 2 0.260 0.830 0.044 0.956
#> TCGA-08-0512-01A-01 2 0.917 0.497 0.332 0.668
#> TCGA-08-0522-01A-01 2 0.814 0.632 0.252 0.748
#> TCGA-12-0619-01A-01 2 0.469 0.811 0.100 0.900
#> TCGA-12-0620-01A-01 2 0.242 0.829 0.040 0.960
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.3695 0.7438 0.880 0.108 0.012
#> TCGA-02-0010-01A-01 1 0.1399 0.7305 0.968 0.028 0.004
#> TCGA-02-0011-01B-01 1 0.3112 0.7495 0.900 0.096 0.004
#> TCGA-02-0014-01A-01 1 0.1267 0.7272 0.972 0.024 0.004
#> TCGA-02-0024-01B-01 1 0.1989 0.7415 0.948 0.048 0.004
#> TCGA-02-0026-01B-01 1 0.0892 0.7208 0.980 0.020 0.000
#> TCGA-02-0028-01A-01 1 0.1643 0.7398 0.956 0.044 0.000
#> TCGA-02-0046-01A-01 1 0.3267 0.7441 0.884 0.116 0.000
#> TCGA-02-0047-01A-01 2 0.6252 0.5955 0.344 0.648 0.008
#> TCGA-02-0048-01A-01 1 0.2959 0.7483 0.900 0.100 0.000
#> TCGA-02-0060-01A-01 1 0.5024 0.6404 0.776 0.220 0.004
#> TCGA-02-0069-01A-01 1 0.1411 0.7358 0.964 0.036 0.000
#> TCGA-02-0074-01A-01 1 0.3686 0.7349 0.860 0.140 0.000
#> TCGA-02-0080-01A-01 1 0.4413 0.7249 0.832 0.160 0.008
#> TCGA-02-0084-01A-03 2 0.7228 0.5520 0.364 0.600 0.036
#> TCGA-02-0087-01A-01 1 0.5580 0.6041 0.736 0.256 0.008
#> TCGA-02-0104-01A-01 1 0.7447 0.4538 0.700 0.160 0.140
#> TCGA-02-0114-01A-01 1 0.2356 0.7487 0.928 0.072 0.000
#> TCGA-02-0281-01A-01 1 0.0892 0.7208 0.980 0.020 0.000
#> TCGA-02-0321-01A-01 2 0.8194 0.5018 0.340 0.572 0.088
#> TCGA-02-0325-01A-01 1 0.2096 0.7409 0.944 0.052 0.004
#> TCGA-02-0338-01A-01 1 0.1267 0.7272 0.972 0.024 0.004
#> TCGA-02-0339-01A-01 1 0.0983 0.7174 0.980 0.016 0.004
#> TCGA-02-0432-01A-02 1 0.4883 0.6767 0.788 0.208 0.004
#> TCGA-02-0439-01A-01 2 0.6330 0.5232 0.396 0.600 0.004
#> TCGA-02-0440-01A-01 1 0.2261 0.7477 0.932 0.068 0.000
#> TCGA-02-0446-01A-01 1 0.6521 -0.2942 0.500 0.496 0.004
#> TCGA-06-0128-01A-01 1 0.5835 0.3820 0.660 0.340 0.000
#> TCGA-06-0129-01A-01 1 0.3816 0.7331 0.852 0.148 0.000
#> TCGA-06-0146-01A-01 1 0.0983 0.7137 0.980 0.016 0.004
#> TCGA-06-0156-01A-01 2 0.6045 0.5517 0.380 0.620 0.000
#> TCGA-06-0166-01A-01 2 0.6264 0.5462 0.380 0.616 0.004
#> TCGA-06-0174-01A-01 1 0.2096 0.7430 0.944 0.052 0.004
#> TCGA-06-0177-01A-01 1 0.4291 0.6743 0.840 0.152 0.008
#> TCGA-06-0238-01A-02 1 0.9664 0.0426 0.460 0.296 0.244
#> TCGA-06-0241-01A-02 1 0.2682 0.7481 0.920 0.076 0.004
#> TCGA-06-0410-01A-01 1 0.5072 0.6746 0.792 0.196 0.012
#> TCGA-06-0413-01A-01 1 0.1267 0.7272 0.972 0.024 0.004
#> TCGA-06-0414-01A-01 1 0.2496 0.7468 0.928 0.068 0.004
#> TCGA-06-0646-01A-01 2 0.6045 0.5457 0.380 0.620 0.000
#> TCGA-06-0648-01A-01 1 0.7202 0.4856 0.716 0.160 0.124
#> TCGA-08-0245-01A-01 1 0.2066 0.7463 0.940 0.060 0.000
#> TCGA-08-0344-01A-01 1 0.4634 0.6931 0.824 0.164 0.012
#> TCGA-08-0347-01A-01 2 0.6282 0.5393 0.384 0.612 0.004
#> TCGA-08-0348-01A-01 1 0.4883 0.6778 0.788 0.208 0.004
#> TCGA-08-0350-01A-01 1 0.5406 0.6369 0.780 0.200 0.020
#> TCGA-08-0353-01A-01 1 0.3267 0.7479 0.884 0.116 0.000
#> TCGA-08-0359-01A-01 2 0.6955 0.2863 0.488 0.496 0.016
#> TCGA-08-0385-01A-01 1 0.7545 0.4586 0.692 0.172 0.136
#> TCGA-08-0517-01A-01 1 0.4842 0.6452 0.776 0.224 0.000
#> TCGA-08-0524-01A-01 1 0.2590 0.7223 0.924 0.072 0.004
#> TCGA-12-0616-01A-01 1 0.7431 0.4784 0.696 0.188 0.116
#> TCGA-12-0618-01A-01 1 0.1267 0.7277 0.972 0.024 0.004
#> TCGA-02-0089-01A-01 2 0.6465 0.6833 0.232 0.724 0.044
#> TCGA-02-0113-01A-01 2 0.5115 0.6818 0.228 0.768 0.004
#> TCGA-02-0115-01A-01 3 0.7927 0.5460 0.176 0.160 0.664
#> TCGA-02-0451-01A-01 2 0.6113 0.6395 0.300 0.688 0.012
#> TCGA-06-0132-01A-02 3 0.1585 0.6969 0.028 0.008 0.964
#> TCGA-06-0133-01A-02 3 0.6001 0.6673 0.072 0.144 0.784
#> TCGA-06-0138-01A-02 2 0.8720 0.4943 0.304 0.560 0.136
#> TCGA-06-0160-01A-01 3 0.2280 0.6971 0.052 0.008 0.940
#> TCGA-06-0162-01A-01 3 0.7368 0.5696 0.200 0.104 0.696
#> TCGA-06-0167-01A-01 3 0.2280 0.6971 0.052 0.008 0.940
#> TCGA-06-0171-01A-02 2 0.9379 0.4454 0.276 0.508 0.216
#> TCGA-06-0173-01A-01 2 0.5859 0.5999 0.344 0.656 0.000
#> TCGA-06-0179-01A-02 3 0.4289 0.7007 0.040 0.092 0.868
#> TCGA-06-0182-01A-01 2 0.8597 0.5182 0.292 0.576 0.132
#> TCGA-06-0185-01A-01 2 0.7104 0.5539 0.360 0.608 0.032
#> TCGA-06-0195-01B-01 3 0.2947 0.6997 0.060 0.020 0.920
#> TCGA-06-0208-01B-01 3 0.9920 -0.0728 0.272 0.360 0.368
#> TCGA-06-0214-01A-02 2 0.5958 0.6409 0.300 0.692 0.008
#> TCGA-06-0219-01A-01 3 0.9932 0.0728 0.284 0.332 0.384
#> TCGA-06-0221-01A-01 3 0.9125 0.3554 0.320 0.164 0.516
#> TCGA-06-0237-01A-02 2 0.9153 0.4638 0.300 0.524 0.176
#> TCGA-06-0240-01A-02 3 0.0661 0.6807 0.008 0.004 0.988
#> TCGA-08-0349-01A-01 2 0.8040 0.5738 0.300 0.608 0.092
#> TCGA-08-0380-01A-01 2 0.7720 0.6470 0.208 0.672 0.120
#> TCGA-08-0386-01A-01 2 0.6111 0.5286 0.396 0.604 0.000
#> TCGA-08-0520-01A-01 2 0.8300 0.5835 0.244 0.620 0.136
#> TCGA-02-0007-01A-01 1 0.6244 -0.0121 0.560 0.440 0.000
#> TCGA-02-0009-01A-01 1 0.5553 0.5877 0.724 0.272 0.004
#> TCGA-02-0016-01A-01 1 0.5553 0.5809 0.724 0.272 0.004
#> TCGA-02-0021-01A-01 2 0.6235 0.3046 0.436 0.564 0.000
#> TCGA-02-0023-01B-01 2 0.8749 0.5018 0.300 0.560 0.140
#> TCGA-02-0027-01A-01 1 0.4682 0.6946 0.804 0.192 0.004
#> TCGA-02-0038-01A-01 2 0.4931 0.6847 0.212 0.784 0.004
#> TCGA-02-0043-01A-01 1 0.5678 0.5113 0.684 0.316 0.000
#> TCGA-02-0070-01A-01 2 0.5905 0.5730 0.352 0.648 0.000
#> TCGA-02-0102-01A-01 1 0.5785 0.4912 0.668 0.332 0.000
#> TCGA-02-0260-01A-03 1 0.1950 0.7048 0.952 0.040 0.008
#> TCGA-02-0269-01B-01 1 0.5167 0.6368 0.792 0.192 0.016
#> TCGA-02-0285-01A-01 2 0.5896 0.6465 0.292 0.700 0.008
#> TCGA-02-0289-01A-01 2 0.6379 0.5697 0.368 0.624 0.008
#> TCGA-02-0290-01A-01 2 0.8834 0.4382 0.316 0.544 0.140
#> TCGA-02-0317-01A-01 1 0.7748 0.4333 0.652 0.252 0.096
#> TCGA-02-0333-01A-02 1 0.5812 0.5368 0.724 0.264 0.012
#> TCGA-02-0422-01A-01 2 0.6008 0.6054 0.332 0.664 0.004
#> TCGA-02-0430-01A-01 1 0.4750 0.6828 0.784 0.216 0.000
#> TCGA-06-0125-01A-01 1 0.5722 0.5588 0.704 0.292 0.004
#> TCGA-06-0126-01A-01 1 0.4784 0.6851 0.796 0.200 0.004
#> TCGA-06-0137-01A-03 1 0.6505 -0.1699 0.528 0.468 0.004
#> TCGA-06-0145-01A-04 2 0.6126 0.5089 0.352 0.644 0.004
#> TCGA-06-0148-01A-01 2 0.5461 0.6598 0.244 0.748 0.008
#> TCGA-06-0187-01A-01 2 0.4887 0.6755 0.228 0.772 0.000
#> TCGA-06-0211-01B-01 2 0.6225 0.4618 0.432 0.568 0.000
#> TCGA-06-0402-01A-01 1 0.5905 0.4478 0.648 0.352 0.000
#> TCGA-08-0246-01A-01 2 0.2625 0.7121 0.084 0.916 0.000
#> TCGA-08-0354-01A-01 2 0.8720 0.4652 0.304 0.560 0.136
#> TCGA-08-0355-01A-01 2 0.7872 0.5977 0.296 0.620 0.084
#> TCGA-08-0357-01A-01 2 0.6189 0.5655 0.364 0.632 0.004
#> TCGA-08-0358-01A-01 1 0.8752 0.2719 0.564 0.292 0.144
#> TCGA-08-0375-01A-01 1 0.1878 0.7286 0.952 0.044 0.004
#> TCGA-08-0511-01A-01 2 0.6057 0.6001 0.340 0.656 0.004
#> TCGA-08-0514-01A-01 2 0.4796 0.6823 0.220 0.780 0.000
#> TCGA-08-0518-01A-01 1 0.6008 0.4078 0.628 0.372 0.000
#> TCGA-08-0529-01A-02 2 0.5254 0.6639 0.264 0.736 0.000
#> TCGA-08-0531-01A-01 2 0.5785 0.6082 0.332 0.668 0.000
#> TCGA-02-0057-01A-01 2 0.6252 0.5218 0.344 0.648 0.008
#> TCGA-02-0004-01A-01 2 0.0000 0.6711 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.5012 0.6890 0.204 0.788 0.008
#> TCGA-02-0025-01A-01 2 0.6271 0.6216 0.088 0.772 0.140
#> TCGA-02-0033-01A-01 2 0.0237 0.6736 0.004 0.996 0.000
#> TCGA-02-0034-01A-01 2 0.0475 0.6710 0.004 0.992 0.004
#> TCGA-02-0039-01A-01 2 0.1643 0.6992 0.044 0.956 0.000
#> TCGA-02-0051-01A-01 2 0.5507 0.6058 0.056 0.808 0.136
#> TCGA-02-0054-01A-01 2 0.4931 0.6847 0.212 0.784 0.004
#> TCGA-02-0055-01A-01 2 0.3412 0.6587 0.000 0.876 0.124
#> TCGA-02-0059-01A-01 2 0.5875 0.5925 0.072 0.792 0.136
#> TCGA-02-0064-01A-01 2 0.5591 0.5596 0.304 0.696 0.000
#> TCGA-02-0075-01A-01 2 0.5678 0.5438 0.316 0.684 0.000
#> TCGA-02-0079-01A-03 2 0.7988 0.5970 0.200 0.656 0.144
#> TCGA-02-0085-01A-01 2 0.7599 0.6384 0.260 0.656 0.084
#> TCGA-02-0086-01A-01 2 0.0475 0.6710 0.004 0.992 0.004
#> TCGA-02-0099-01A-01 2 0.4702 0.6849 0.212 0.788 0.000
#> TCGA-02-0106-01A-01 2 0.0237 0.6736 0.004 0.996 0.000
#> TCGA-02-0107-01A-01 2 0.1337 0.6804 0.012 0.972 0.016
#> TCGA-02-0111-01A-01 2 0.3551 0.6563 0.000 0.868 0.132
#> TCGA-02-0326-01A-01 2 0.9449 0.2450 0.384 0.436 0.180
#> TCGA-02-0337-01A-01 2 0.1765 0.6976 0.040 0.956 0.004
#> TCGA-06-0122-01A-01 2 0.5733 0.5342 0.324 0.676 0.000
#> TCGA-06-0124-01A-01 2 0.5591 0.5596 0.304 0.696 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.6711 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.6711 0.000 1.000 0.000
#> TCGA-06-0143-01A-01 2 0.6180 0.3020 0.416 0.584 0.000
#> TCGA-06-0147-01A-01 2 0.0237 0.6736 0.004 0.996 0.000
#> TCGA-06-0149-01A-05 2 0.1765 0.6969 0.040 0.956 0.004
#> TCGA-06-0152-01A-02 2 0.9136 0.2493 0.400 0.456 0.144
#> TCGA-06-0154-01A-02 2 0.0475 0.6710 0.004 0.992 0.004
#> TCGA-06-0164-01A-01 2 0.0475 0.6710 0.004 0.992 0.004
#> TCGA-06-0175-01A-01 2 0.5397 0.6401 0.280 0.720 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.6711 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.4914 0.7108 0.088 0.844 0.068
#> TCGA-06-0189-01A-05 2 0.3851 0.6513 0.004 0.860 0.136
#> TCGA-06-0190-01A-01 2 0.0237 0.6679 0.000 0.996 0.004
#> TCGA-06-0194-01A-01 2 0.0237 0.6679 0.000 0.996 0.004
#> TCGA-06-0197-01A-02 2 0.3340 0.6598 0.000 0.880 0.120
#> TCGA-06-0210-01A-01 2 0.0475 0.6710 0.004 0.992 0.004
#> TCGA-06-0397-01A-01 2 0.4178 0.6967 0.172 0.828 0.000
#> TCGA-06-0409-01A-02 2 0.0237 0.6736 0.004 0.996 0.000
#> TCGA-06-0412-01A-01 2 0.1129 0.6837 0.020 0.976 0.004
#> TCGA-06-0644-01A-02 2 0.0237 0.6690 0.004 0.996 0.000
#> TCGA-06-0645-01A-01 2 0.1529 0.6974 0.040 0.960 0.000
#> TCGA-08-0346-01A-01 2 0.1289 0.6936 0.032 0.968 0.000
#> TCGA-08-0352-01A-01 2 0.5109 0.6959 0.212 0.780 0.008
#> TCGA-08-0360-01A-01 2 0.0000 0.6711 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.7860 0.6243 0.204 0.664 0.132
#> TCGA-08-0392-01A-01 2 0.8650 0.4585 0.292 0.572 0.136
#> TCGA-08-0509-01A-01 2 0.1753 0.7002 0.048 0.952 0.000
#> TCGA-08-0510-01A-01 2 0.5810 0.5268 0.336 0.664 0.000
#> TCGA-08-0512-01A-01 2 0.0475 0.6710 0.004 0.992 0.004
#> TCGA-08-0522-01A-01 2 0.0475 0.6710 0.004 0.992 0.004
#> TCGA-12-0619-01A-01 2 0.4351 0.7007 0.168 0.828 0.004
#> TCGA-12-0620-01A-01 2 0.8572 0.4982 0.288 0.580 0.132
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.4853 0.57859 0.744 0.220 0.036 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.78389 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.3421 0.72167 0.868 0.088 0.044 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.78389 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.78389 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0524 0.78449 0.988 0.004 0.008 0.000
#> TCGA-02-0028-01A-01 1 0.0469 0.78475 0.988 0.000 0.012 0.000
#> TCGA-02-0046-01A-01 1 0.0188 0.78458 0.996 0.004 0.000 0.000
#> TCGA-02-0047-01A-01 2 0.4595 0.66789 0.184 0.776 0.040 0.000
#> TCGA-02-0048-01A-01 1 0.1867 0.75671 0.928 0.072 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.5929 0.36304 0.596 0.356 0.048 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.78389 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0188 0.78396 0.996 0.000 0.004 0.000
#> TCGA-02-0080-01A-01 1 0.5118 0.67215 0.736 0.040 0.220 0.004
#> TCGA-02-0084-01A-03 2 0.5212 0.61285 0.004 0.588 0.404 0.004
#> TCGA-02-0087-01A-01 1 0.7264 0.49199 0.564 0.220 0.212 0.004
#> TCGA-02-0104-01A-01 3 0.4955 0.44295 0.344 0.008 0.648 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.78389 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0524 0.78449 0.988 0.004 0.008 0.000
#> TCGA-02-0321-01A-01 2 0.7188 0.54095 0.172 0.536 0.292 0.000
#> TCGA-02-0325-01A-01 1 0.3676 0.69855 0.820 0.004 0.172 0.004
#> TCGA-02-0338-01A-01 1 0.0000 0.78389 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0657 0.78391 0.984 0.004 0.012 0.000
#> TCGA-02-0432-01A-02 1 0.6624 0.60179 0.640 0.152 0.204 0.004
#> TCGA-02-0439-01A-01 2 0.5982 0.60004 0.112 0.684 0.204 0.000
#> TCGA-02-0440-01A-01 1 0.0188 0.78458 0.996 0.004 0.000 0.000
#> TCGA-02-0446-01A-01 2 0.4669 0.65990 0.200 0.764 0.036 0.000
#> TCGA-06-0128-01A-01 1 0.6052 0.24099 0.556 0.396 0.048 0.000
#> TCGA-06-0129-01A-01 1 0.1452 0.78071 0.956 0.008 0.036 0.000
#> TCGA-06-0146-01A-01 1 0.3636 0.70061 0.820 0.008 0.172 0.000
#> TCGA-06-0156-01A-01 2 0.4508 0.67014 0.184 0.780 0.036 0.000
#> TCGA-06-0166-01A-01 2 0.4057 0.69210 0.160 0.812 0.028 0.000
#> TCGA-06-0174-01A-01 1 0.0000 0.78389 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0804 0.77958 0.980 0.008 0.012 0.000
#> TCGA-06-0238-01A-02 3 0.6052 0.38796 0.176 0.124 0.696 0.004
#> TCGA-06-0241-01A-02 1 0.1637 0.76562 0.940 0.060 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.5624 0.46114 0.668 0.280 0.052 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.78389 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.1211 0.77223 0.960 0.040 0.000 0.000
#> TCGA-06-0646-01A-01 2 0.4706 0.66383 0.224 0.748 0.028 0.000
#> TCGA-06-0648-01A-01 3 0.4955 0.44295 0.344 0.008 0.648 0.000
#> TCGA-08-0245-01A-01 1 0.0188 0.78422 0.996 0.004 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.2198 0.73323 0.920 0.008 0.072 0.000
#> TCGA-08-0347-01A-01 2 0.4590 0.66401 0.192 0.772 0.036 0.000
#> TCGA-08-0348-01A-01 1 0.4103 0.53378 0.744 0.256 0.000 0.000
#> TCGA-08-0350-01A-01 3 0.5713 0.23111 0.360 0.036 0.604 0.000
#> TCGA-08-0353-01A-01 1 0.3196 0.69872 0.856 0.136 0.008 0.000
#> TCGA-08-0359-01A-01 2 0.5987 0.19054 0.440 0.520 0.040 0.000
#> TCGA-08-0385-01A-01 3 0.5018 0.45389 0.332 0.012 0.656 0.000
#> TCGA-08-0517-01A-01 1 0.4781 0.46226 0.660 0.336 0.004 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.78389 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 3 0.5291 0.46380 0.324 0.024 0.652 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.78389 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.4804 0.67649 0.160 0.776 0.064 0.000
#> TCGA-02-0113-01A-01 2 0.3056 0.73097 0.072 0.888 0.040 0.000
#> TCGA-02-0115-01A-01 4 0.7183 0.42534 0.172 0.204 0.016 0.608
#> TCGA-02-0451-01A-01 2 0.4756 0.67029 0.176 0.772 0.052 0.000
#> TCGA-06-0132-01A-02 4 0.1474 0.76281 0.052 0.000 0.000 0.948
#> TCGA-06-0133-01A-02 4 0.4376 0.67916 0.176 0.012 0.016 0.796
#> TCGA-06-0138-01A-02 2 0.8012 0.27913 0.176 0.504 0.292 0.028
#> TCGA-06-0160-01A-01 4 0.0336 0.76065 0.008 0.000 0.000 0.992
#> TCGA-06-0162-01A-01 4 0.9259 0.17195 0.176 0.120 0.288 0.416
#> TCGA-06-0167-01A-01 4 0.0336 0.76065 0.008 0.000 0.000 0.992
#> TCGA-06-0171-01A-02 2 0.8913 0.28167 0.184 0.496 0.120 0.200
#> TCGA-06-0173-01A-01 2 0.4508 0.66834 0.184 0.780 0.036 0.000
#> TCGA-06-0179-01A-02 4 0.3538 0.70455 0.160 0.004 0.004 0.832
#> TCGA-06-0182-01A-01 2 0.5533 0.55035 0.072 0.708 0.220 0.000
#> TCGA-06-0185-01A-01 2 0.4756 0.67085 0.176 0.772 0.052 0.000
#> TCGA-06-0195-01B-01 4 0.0967 0.76298 0.016 0.004 0.004 0.976
#> TCGA-06-0208-01B-01 2 0.8461 -0.05836 0.184 0.416 0.040 0.360
#> TCGA-06-0214-01A-02 2 0.4595 0.66766 0.184 0.776 0.040 0.000
#> TCGA-06-0219-01A-01 3 0.9320 -0.01459 0.180 0.128 0.416 0.276
#> TCGA-06-0221-01A-01 3 0.8960 0.11993 0.180 0.120 0.488 0.212
#> TCGA-06-0237-01A-02 2 0.9000 0.29265 0.164 0.492 0.148 0.196
#> TCGA-06-0240-01A-02 4 0.0336 0.76065 0.008 0.000 0.000 0.992
#> TCGA-08-0349-01A-01 2 0.6025 0.60819 0.172 0.688 0.140 0.000
#> TCGA-08-0380-01A-01 2 0.4713 0.68275 0.052 0.776 0.172 0.000
#> TCGA-08-0386-01A-01 2 0.5599 0.51321 0.316 0.644 0.040 0.000
#> TCGA-08-0520-01A-01 2 0.6346 0.55720 0.116 0.640 0.244 0.000
#> TCGA-02-0007-01A-01 2 0.6607 0.01443 0.444 0.476 0.080 0.000
#> TCGA-02-0009-01A-01 1 0.4289 0.70321 0.796 0.032 0.172 0.000
#> TCGA-02-0016-01A-01 1 0.7617 0.27569 0.424 0.372 0.204 0.000
#> TCGA-02-0021-01A-01 2 0.5682 0.00718 0.456 0.520 0.024 0.000
#> TCGA-02-0023-01B-01 2 0.5237 0.52072 0.016 0.628 0.356 0.000
#> TCGA-02-0027-01A-01 1 0.5248 0.68850 0.748 0.088 0.164 0.000
#> TCGA-02-0038-01A-01 2 0.1762 0.74734 0.004 0.944 0.048 0.004
#> TCGA-02-0043-01A-01 1 0.4012 0.64108 0.800 0.184 0.016 0.000
#> TCGA-02-0070-01A-01 2 0.5228 0.68173 0.120 0.756 0.124 0.000
#> TCGA-02-0102-01A-01 1 0.4713 0.66886 0.776 0.172 0.052 0.000
#> TCGA-02-0260-01A-03 1 0.3992 0.68019 0.800 0.008 0.188 0.004
#> TCGA-02-0269-01B-01 3 0.5937 -0.08512 0.456 0.028 0.512 0.004
#> TCGA-02-0285-01A-01 2 0.4122 0.66352 0.004 0.760 0.236 0.000
#> TCGA-02-0289-01A-01 2 0.5849 0.64976 0.052 0.656 0.288 0.004
#> TCGA-02-0290-01A-01 3 0.3801 0.60658 0.000 0.220 0.780 0.000
#> TCGA-02-0317-01A-01 3 0.2007 0.57449 0.036 0.020 0.940 0.004
#> TCGA-02-0333-01A-02 1 0.7833 0.16420 0.416 0.216 0.364 0.004
#> TCGA-02-0422-01A-01 2 0.4121 0.71972 0.020 0.796 0.184 0.000
#> TCGA-02-0430-01A-01 1 0.4319 0.61625 0.760 0.228 0.012 0.000
#> TCGA-06-0125-01A-01 1 0.3853 0.70460 0.820 0.020 0.160 0.000
#> TCGA-06-0126-01A-01 1 0.5763 0.65975 0.700 0.096 0.204 0.000
#> TCGA-06-0137-01A-03 2 0.7558 -0.04454 0.360 0.444 0.196 0.000
#> TCGA-06-0145-01A-04 2 0.3808 0.69662 0.012 0.812 0.176 0.000
#> TCGA-06-0148-01A-01 2 0.3428 0.74541 0.012 0.844 0.144 0.000
#> TCGA-06-0187-01A-01 2 0.0779 0.75192 0.004 0.980 0.016 0.000
#> TCGA-06-0211-01B-01 2 0.5249 0.61733 0.248 0.708 0.044 0.000
#> TCGA-06-0402-01A-01 1 0.4240 0.63322 0.784 0.200 0.012 0.004
#> TCGA-08-0246-01A-01 2 0.2530 0.74902 0.000 0.888 0.112 0.000
#> TCGA-08-0354-01A-01 3 0.3801 0.60540 0.000 0.220 0.780 0.000
#> TCGA-08-0355-01A-01 2 0.4428 0.64372 0.004 0.720 0.276 0.000
#> TCGA-08-0357-01A-01 2 0.5257 0.67005 0.144 0.752 0.104 0.000
#> TCGA-08-0358-01A-01 3 0.2123 0.58194 0.032 0.028 0.936 0.004
#> TCGA-08-0375-01A-01 1 0.4370 0.69413 0.800 0.044 0.156 0.000
#> TCGA-08-0511-01A-01 2 0.4829 0.68500 0.068 0.776 0.156 0.000
#> TCGA-08-0514-01A-01 2 0.1004 0.75259 0.004 0.972 0.024 0.000
#> TCGA-08-0518-01A-01 1 0.4671 0.62293 0.752 0.220 0.028 0.000
#> TCGA-08-0529-01A-02 2 0.2060 0.75339 0.016 0.932 0.052 0.000
#> TCGA-08-0531-01A-01 2 0.3958 0.70909 0.032 0.824 0.144 0.000
#> TCGA-02-0057-01A-01 2 0.4098 0.67894 0.012 0.784 0.204 0.000
#> TCGA-02-0004-01A-01 2 0.3052 0.73582 0.000 0.860 0.136 0.004
#> TCGA-02-0006-01B-01 2 0.1296 0.74873 0.004 0.964 0.028 0.004
#> TCGA-02-0025-01A-01 3 0.3837 0.60327 0.000 0.224 0.776 0.000
#> TCGA-02-0033-01A-01 2 0.2888 0.74149 0.000 0.872 0.124 0.004
#> TCGA-02-0034-01A-01 2 0.2888 0.74124 0.000 0.872 0.124 0.004
#> TCGA-02-0039-01A-01 2 0.4319 0.71264 0.012 0.760 0.228 0.000
#> TCGA-02-0051-01A-01 3 0.4053 0.59765 0.000 0.228 0.768 0.004
#> TCGA-02-0054-01A-01 2 0.1296 0.74873 0.004 0.964 0.028 0.004
#> TCGA-02-0055-01A-01 2 0.3208 0.72681 0.000 0.848 0.148 0.004
#> TCGA-02-0059-01A-01 3 0.4053 0.59765 0.000 0.228 0.768 0.004
#> TCGA-02-0064-01A-01 2 0.2921 0.74426 0.000 0.860 0.140 0.000
#> TCGA-02-0075-01A-01 2 0.2999 0.74506 0.000 0.864 0.132 0.004
#> TCGA-02-0079-01A-03 3 0.1661 0.58052 0.000 0.052 0.944 0.004
#> TCGA-02-0085-01A-01 2 0.5071 0.67920 0.144 0.772 0.080 0.004
#> TCGA-02-0086-01A-01 2 0.2888 0.74149 0.000 0.872 0.124 0.004
#> TCGA-02-0099-01A-01 2 0.1296 0.74942 0.004 0.964 0.028 0.004
#> TCGA-02-0106-01A-01 2 0.2888 0.74149 0.000 0.872 0.124 0.004
#> TCGA-02-0107-01A-01 2 0.1004 0.75265 0.000 0.972 0.024 0.004
#> TCGA-02-0111-01A-01 2 0.3052 0.73591 0.000 0.860 0.136 0.004
#> TCGA-02-0326-01A-01 3 0.1004 0.56134 0.000 0.024 0.972 0.004
#> TCGA-02-0337-01A-01 2 0.3444 0.74176 0.000 0.816 0.184 0.000
#> TCGA-06-0122-01A-01 2 0.3105 0.74477 0.004 0.856 0.140 0.000
#> TCGA-06-0124-01A-01 2 0.2921 0.74528 0.000 0.860 0.140 0.000
#> TCGA-06-0130-01A-01 2 0.2831 0.74260 0.000 0.876 0.120 0.004
#> TCGA-06-0139-01A-01 2 0.2831 0.74260 0.000 0.876 0.120 0.004
#> TCGA-06-0143-01A-01 2 0.4491 0.71230 0.060 0.800 0.140 0.000
#> TCGA-06-0147-01A-01 2 0.2999 0.74402 0.000 0.864 0.132 0.004
#> TCGA-06-0149-01A-05 2 0.3024 0.74568 0.000 0.852 0.148 0.000
#> TCGA-06-0152-01A-02 3 0.1661 0.58142 0.000 0.052 0.944 0.004
#> TCGA-06-0154-01A-02 2 0.2888 0.74149 0.000 0.872 0.124 0.004
#> TCGA-06-0164-01A-01 2 0.2831 0.74260 0.000 0.876 0.120 0.004
#> TCGA-06-0175-01A-01 2 0.4423 0.67321 0.176 0.788 0.036 0.000
#> TCGA-06-0176-01A-03 2 0.2944 0.73960 0.000 0.868 0.128 0.004
#> TCGA-06-0184-01A-01 2 0.2522 0.74039 0.016 0.908 0.076 0.000
#> TCGA-06-0189-01A-05 3 0.4252 0.57618 0.000 0.252 0.744 0.004
#> TCGA-06-0190-01A-01 2 0.2888 0.74149 0.000 0.872 0.124 0.004
#> TCGA-06-0194-01A-01 2 0.2944 0.73960 0.000 0.868 0.128 0.004
#> TCGA-06-0197-01A-02 2 0.3052 0.73591 0.000 0.860 0.136 0.004
#> TCGA-06-0210-01A-01 2 0.2888 0.74149 0.000 0.872 0.124 0.004
#> TCGA-06-0397-01A-01 2 0.2831 0.74322 0.000 0.876 0.120 0.004
#> TCGA-06-0409-01A-02 2 0.2760 0.74394 0.000 0.872 0.128 0.000
#> TCGA-06-0412-01A-01 2 0.2831 0.74260 0.000 0.876 0.120 0.004
#> TCGA-06-0644-01A-02 2 0.4053 0.63685 0.000 0.768 0.228 0.004
#> TCGA-06-0645-01A-01 2 0.2944 0.74563 0.004 0.868 0.128 0.000
#> TCGA-08-0346-01A-01 2 0.3219 0.72915 0.000 0.836 0.164 0.000
#> TCGA-08-0352-01A-01 2 0.5035 0.69697 0.052 0.744 0.204 0.000
#> TCGA-08-0360-01A-01 2 0.2704 0.74361 0.000 0.876 0.124 0.000
#> TCGA-08-0390-01A-01 2 0.6790 0.51607 0.168 0.604 0.228 0.000
#> TCGA-08-0392-01A-01 3 0.3982 0.60264 0.000 0.220 0.776 0.004
#> TCGA-08-0509-01A-01 2 0.1743 0.75586 0.004 0.940 0.056 0.000
#> TCGA-08-0510-01A-01 2 0.1637 0.75502 0.000 0.940 0.060 0.000
#> TCGA-08-0512-01A-01 2 0.2831 0.74260 0.000 0.876 0.120 0.004
#> TCGA-08-0522-01A-01 2 0.2944 0.73960 0.000 0.868 0.128 0.004
#> TCGA-12-0619-01A-01 2 0.2888 0.74180 0.000 0.872 0.124 0.004
#> TCGA-12-0620-01A-01 3 0.3801 0.60540 0.000 0.220 0.780 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 3 0.4367 0.4616 0.416 0.004 0.580 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0162 0.6682 0.996 0.000 0.004 0.000 0.000
#> TCGA-02-0011-01B-01 3 0.4688 0.4001 0.456 0.008 0.532 0.000 0.004
#> TCGA-02-0014-01A-01 1 0.0000 0.6688 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.2605 0.6369 0.852 0.000 0.148 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.6688 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0290 0.6681 0.992 0.000 0.008 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.3949 0.1895 0.668 0.000 0.332 0.000 0.000
#> TCGA-02-0047-01A-01 3 0.4986 0.6593 0.176 0.104 0.716 0.000 0.004
#> TCGA-02-0048-01A-01 3 0.3966 0.5222 0.336 0.000 0.664 0.000 0.000
#> TCGA-02-0060-01A-01 3 0.4236 0.5827 0.248 0.016 0.728 0.000 0.008
#> TCGA-02-0069-01A-01 1 0.0290 0.6675 0.992 0.000 0.008 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0510 0.6661 0.984 0.000 0.016 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.6841 0.3354 0.440 0.016 0.368 0.000 0.176
#> TCGA-02-0084-01A-03 2 0.6561 0.0998 0.000 0.424 0.204 0.000 0.372
#> TCGA-02-0087-01A-01 1 0.6990 0.4729 0.540 0.048 0.236 0.000 0.176
#> TCGA-02-0104-01A-01 5 0.5644 0.5194 0.200 0.008 0.136 0.000 0.656
#> TCGA-02-0114-01A-01 1 0.2690 0.5812 0.844 0.000 0.156 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.1907 0.6535 0.928 0.000 0.028 0.000 0.044
#> TCGA-02-0321-01A-01 2 0.6322 0.3876 0.152 0.600 0.224 0.000 0.024
#> TCGA-02-0325-01A-01 1 0.3495 0.5570 0.812 0.000 0.028 0.000 0.160
#> TCGA-02-0338-01A-01 1 0.0000 0.6688 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0324 0.6672 0.992 0.000 0.004 0.000 0.004
#> TCGA-02-0432-01A-02 3 0.5176 0.5302 0.096 0.016 0.716 0.000 0.172
#> TCGA-02-0439-01A-01 3 0.4846 0.6125 0.016 0.088 0.748 0.000 0.148
#> TCGA-02-0440-01A-01 1 0.4161 0.2892 0.608 0.000 0.392 0.000 0.000
#> TCGA-02-0446-01A-01 3 0.4752 0.6522 0.184 0.092 0.724 0.000 0.000
#> TCGA-06-0128-01A-01 3 0.4708 0.4417 0.436 0.016 0.548 0.000 0.000
#> TCGA-06-0129-01A-01 1 0.1121 0.6593 0.956 0.000 0.044 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.3495 0.5570 0.812 0.000 0.028 0.000 0.160
#> TCGA-06-0156-01A-01 3 0.4852 0.6564 0.184 0.100 0.716 0.000 0.000
#> TCGA-06-0166-01A-01 3 0.5599 0.6309 0.172 0.168 0.656 0.000 0.004
#> TCGA-06-0174-01A-01 1 0.4227 0.2104 0.580 0.000 0.420 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.6654 0.1492 0.488 0.008 0.196 0.000 0.308
#> TCGA-06-0238-01A-02 5 0.3849 0.5503 0.168 0.004 0.012 0.016 0.800
#> TCGA-06-0241-01A-02 3 0.4192 0.3459 0.404 0.000 0.596 0.000 0.000
#> TCGA-06-0410-01A-01 3 0.4774 0.2163 0.444 0.012 0.540 0.000 0.004
#> TCGA-06-0413-01A-01 1 0.0000 0.6688 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 3 0.4060 0.4464 0.360 0.000 0.640 0.000 0.000
#> TCGA-06-0646-01A-01 2 0.4958 0.5372 0.036 0.592 0.372 0.000 0.000
#> TCGA-06-0648-01A-01 5 0.6322 0.4469 0.208 0.012 0.200 0.000 0.580
#> TCGA-08-0245-01A-01 1 0.3266 0.6041 0.796 0.004 0.200 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.4030 0.5561 0.736 0.008 0.248 0.000 0.008
#> TCGA-08-0347-01A-01 3 0.4902 0.6556 0.172 0.100 0.724 0.000 0.004
#> TCGA-08-0348-01A-01 1 0.4572 0.4778 0.684 0.036 0.280 0.000 0.000
#> TCGA-08-0350-01A-01 5 0.6662 0.4641 0.092 0.052 0.320 0.000 0.536
#> TCGA-08-0353-01A-01 1 0.4789 0.5181 0.584 0.024 0.392 0.000 0.000
#> TCGA-08-0359-01A-01 3 0.4600 0.6153 0.220 0.044 0.728 0.000 0.008
#> TCGA-08-0385-01A-01 5 0.5356 0.5541 0.176 0.016 0.108 0.000 0.700
#> TCGA-08-0517-01A-01 3 0.3814 0.5617 0.276 0.004 0.720 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.4677 0.5556 0.732 0.004 0.196 0.000 0.068
#> TCGA-12-0616-01A-01 5 0.6506 0.4806 0.172 0.024 0.228 0.000 0.576
#> TCGA-12-0618-01A-01 1 0.3074 0.6044 0.804 0.000 0.196 0.000 0.000
#> TCGA-02-0089-01A-01 3 0.6234 0.6515 0.156 0.232 0.596 0.000 0.016
#> TCGA-02-0113-01A-01 3 0.5010 0.6450 0.088 0.224 0.688 0.000 0.000
#> TCGA-02-0115-01A-01 4 0.5581 0.6296 0.168 0.060 0.044 0.716 0.012
#> TCGA-02-0451-01A-01 3 0.5647 0.6690 0.164 0.156 0.668 0.000 0.012
#> TCGA-06-0132-01A-02 4 0.1492 0.8217 0.040 0.000 0.004 0.948 0.008
#> TCGA-06-0133-01A-02 4 0.4116 0.7189 0.164 0.012 0.024 0.792 0.008
#> TCGA-06-0138-01A-02 3 0.6285 0.6283 0.168 0.084 0.652 0.000 0.096
#> TCGA-06-0160-01A-01 4 0.0000 0.8136 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0162-01A-01 3 0.8703 -0.0675 0.164 0.008 0.284 0.264 0.280
#> TCGA-06-0167-01A-01 4 0.0000 0.8136 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0171-01A-02 3 0.6016 0.6425 0.168 0.100 0.680 0.044 0.008
#> TCGA-06-0173-01A-01 3 0.5083 0.6629 0.184 0.120 0.696 0.000 0.000
#> TCGA-06-0179-01A-02 4 0.3327 0.7472 0.160 0.008 0.004 0.824 0.004
#> TCGA-06-0182-01A-01 3 0.8126 0.3132 0.116 0.300 0.372 0.000 0.212
#> TCGA-06-0185-01A-01 3 0.4949 0.6580 0.164 0.100 0.728 0.000 0.008
#> TCGA-06-0195-01B-01 4 0.1768 0.7937 0.000 0.004 0.072 0.924 0.000
#> TCGA-06-0208-01B-01 3 0.7304 0.3930 0.180 0.056 0.488 0.276 0.000
#> TCGA-06-0214-01A-02 3 0.5339 0.6673 0.176 0.152 0.672 0.000 0.000
#> TCGA-06-0219-01A-01 5 0.8803 0.0140 0.168 0.016 0.284 0.212 0.320
#> TCGA-06-0221-01A-01 5 0.8063 0.1339 0.168 0.000 0.176 0.216 0.440
#> TCGA-06-0237-01A-02 3 0.5152 0.6569 0.164 0.104 0.720 0.004 0.008
#> TCGA-06-0240-01A-02 4 0.0000 0.8136 0.000 0.000 0.000 1.000 0.000
#> TCGA-08-0349-01A-01 3 0.5152 0.6573 0.164 0.104 0.720 0.004 0.008
#> TCGA-08-0380-01A-01 3 0.4650 0.6499 0.036 0.128 0.776 0.000 0.060
#> TCGA-08-0386-01A-01 3 0.4670 0.6416 0.200 0.076 0.724 0.000 0.000
#> TCGA-08-0520-01A-01 3 0.6583 0.5427 0.072 0.112 0.612 0.000 0.204
#> TCGA-02-0007-01A-01 3 0.3170 0.6124 0.104 0.036 0.856 0.000 0.004
#> TCGA-02-0009-01A-01 3 0.5611 0.1790 0.284 0.004 0.616 0.000 0.096
#> TCGA-02-0016-01A-01 3 0.5190 0.5322 0.100 0.016 0.716 0.000 0.168
#> TCGA-02-0021-01A-01 3 0.5486 0.1892 0.260 0.096 0.640 0.000 0.004
#> TCGA-02-0023-01B-01 2 0.6431 0.1352 0.000 0.436 0.388 0.000 0.176
#> TCGA-02-0027-01A-01 1 0.5088 0.3755 0.572 0.004 0.392 0.000 0.032
#> TCGA-02-0038-01A-01 3 0.3816 0.4777 0.000 0.304 0.696 0.000 0.000
#> TCGA-02-0043-01A-01 1 0.4096 0.4891 0.724 0.012 0.260 0.000 0.004
#> TCGA-02-0070-01A-01 2 0.4536 0.6045 0.008 0.640 0.344 0.000 0.008
#> TCGA-02-0102-01A-01 3 0.4655 -0.3023 0.476 0.012 0.512 0.000 0.000
#> TCGA-02-0260-01A-03 1 0.4704 0.4924 0.696 0.012 0.028 0.000 0.264
#> TCGA-02-0269-01B-01 5 0.5917 0.4531 0.096 0.040 0.204 0.000 0.660
#> TCGA-02-0285-01A-01 2 0.3999 0.6129 0.000 0.656 0.344 0.000 0.000
#> TCGA-02-0289-01A-01 2 0.6141 0.4698 0.004 0.576 0.248 0.000 0.172
#> TCGA-02-0290-01A-01 5 0.3914 0.5783 0.000 0.048 0.164 0.000 0.788
#> TCGA-02-0317-01A-01 5 0.3164 0.5900 0.000 0.044 0.104 0.000 0.852
#> TCGA-02-0333-01A-02 5 0.7590 0.1994 0.212 0.092 0.204 0.000 0.492
#> TCGA-02-0422-01A-01 2 0.4201 0.5285 0.000 0.592 0.408 0.000 0.000
#> TCGA-02-0430-01A-01 1 0.4599 0.5669 0.688 0.040 0.272 0.000 0.000
#> TCGA-06-0125-01A-01 1 0.4015 0.4945 0.724 0.008 0.264 0.000 0.004
#> TCGA-06-0126-01A-01 1 0.6441 0.1707 0.424 0.004 0.420 0.000 0.152
#> TCGA-06-0137-01A-03 3 0.5739 0.4606 0.244 0.004 0.624 0.000 0.128
#> TCGA-06-0145-01A-04 3 0.3978 0.4367 0.148 0.052 0.796 0.000 0.004
#> TCGA-06-0148-01A-01 2 0.2966 0.7320 0.000 0.816 0.184 0.000 0.000
#> TCGA-06-0187-01A-01 3 0.3796 0.4789 0.000 0.300 0.700 0.000 0.000
#> TCGA-06-0211-01B-01 3 0.4852 0.6521 0.184 0.100 0.716 0.000 0.000
#> TCGA-06-0402-01A-01 1 0.4689 0.4459 0.560 0.016 0.424 0.000 0.000
#> TCGA-08-0246-01A-01 2 0.4306 0.2098 0.000 0.508 0.492 0.000 0.000
#> TCGA-08-0354-01A-01 5 0.3803 0.5967 0.000 0.140 0.056 0.000 0.804
#> TCGA-08-0355-01A-01 2 0.6217 0.3642 0.000 0.520 0.316 0.000 0.164
#> TCGA-08-0357-01A-01 3 0.4550 0.6559 0.100 0.136 0.760 0.000 0.004
#> TCGA-08-0358-01A-01 5 0.0798 0.5877 0.000 0.016 0.008 0.000 0.976
#> TCGA-08-0375-01A-01 1 0.5344 0.5149 0.580 0.016 0.372 0.000 0.032
#> TCGA-08-0511-01A-01 3 0.5563 0.6608 0.092 0.116 0.720 0.000 0.072
#> TCGA-08-0514-01A-01 3 0.3480 0.5428 0.000 0.248 0.752 0.000 0.000
#> TCGA-08-0518-01A-01 1 0.4920 0.4619 0.584 0.032 0.384 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.3612 0.4641 0.000 0.268 0.732 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.2536 0.6212 0.000 0.128 0.868 0.000 0.004
#> TCGA-02-0057-01A-01 3 0.4691 0.5081 0.000 0.276 0.680 0.000 0.044
#> TCGA-02-0004-01A-01 2 0.2280 0.6851 0.000 0.880 0.000 0.000 0.120
#> TCGA-02-0006-01B-01 3 0.4210 0.4172 0.000 0.412 0.588 0.000 0.000
#> TCGA-02-0025-01A-01 5 0.3888 0.5937 0.000 0.148 0.056 0.000 0.796
#> TCGA-02-0033-01A-01 2 0.0162 0.7496 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0034-01A-01 2 0.0703 0.7564 0.000 0.976 0.024 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.4299 0.4332 0.000 0.608 0.388 0.000 0.004
#> TCGA-02-0051-01A-01 5 0.3452 0.5448 0.000 0.244 0.000 0.000 0.756
#> TCGA-02-0054-01A-01 3 0.4150 0.4283 0.000 0.388 0.612 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.2471 0.6720 0.000 0.864 0.000 0.000 0.136
#> TCGA-02-0059-01A-01 5 0.3074 0.5746 0.000 0.196 0.000 0.000 0.804
#> TCGA-02-0064-01A-01 2 0.3274 0.7127 0.000 0.780 0.220 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.3628 0.6928 0.012 0.772 0.216 0.000 0.000
#> TCGA-02-0079-01A-03 5 0.2464 0.5842 0.000 0.096 0.016 0.000 0.888
#> TCGA-02-0085-01A-01 3 0.6336 0.6524 0.148 0.232 0.596 0.000 0.024
#> TCGA-02-0086-01A-01 2 0.3305 0.5193 0.000 0.776 0.224 0.000 0.000
#> TCGA-02-0099-01A-01 3 0.4161 0.4284 0.000 0.392 0.608 0.000 0.000
#> TCGA-02-0106-01A-01 2 0.0162 0.7496 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0107-01A-01 3 0.4227 0.3873 0.000 0.420 0.580 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.3519 0.5911 0.000 0.776 0.008 0.000 0.216
#> TCGA-02-0326-01A-01 5 0.1095 0.5805 0.000 0.012 0.008 0.012 0.968
#> TCGA-02-0337-01A-01 2 0.2891 0.7336 0.000 0.824 0.176 0.000 0.000
#> TCGA-06-0122-01A-01 3 0.6736 -0.2522 0.196 0.344 0.452 0.000 0.008
#> TCGA-06-0124-01A-01 2 0.3242 0.7204 0.000 0.784 0.216 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0162 0.7496 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0139-01A-01 2 0.0162 0.7496 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0143-01A-01 2 0.6745 0.4166 0.228 0.480 0.284 0.000 0.008
#> TCGA-06-0147-01A-01 2 0.1608 0.7607 0.000 0.928 0.072 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.2929 0.7305 0.000 0.820 0.180 0.000 0.000
#> TCGA-06-0152-01A-02 5 0.3146 0.6128 0.000 0.028 0.128 0.000 0.844
#> TCGA-06-0154-01A-02 2 0.1608 0.7601 0.000 0.928 0.072 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0880 0.7517 0.000 0.968 0.032 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.5700 0.6608 0.176 0.196 0.628 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.0290 0.7474 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0184-01A-01 3 0.3816 0.4711 0.000 0.304 0.696 0.000 0.000
#> TCGA-06-0189-01A-05 2 0.3752 0.4451 0.000 0.708 0.000 0.000 0.292
#> TCGA-06-0190-01A-01 2 0.0162 0.7496 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0194-01A-01 2 0.0162 0.7496 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0197-01A-02 2 0.3074 0.6118 0.000 0.804 0.000 0.000 0.196
#> TCGA-06-0210-01A-01 2 0.1121 0.7592 0.000 0.956 0.044 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.2230 0.7526 0.000 0.884 0.116 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.1732 0.7595 0.000 0.920 0.080 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.1608 0.7600 0.000 0.928 0.072 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.2605 0.6608 0.000 0.852 0.000 0.000 0.148
#> TCGA-06-0645-01A-01 2 0.2773 0.7340 0.000 0.836 0.164 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.5413 0.6426 0.000 0.664 0.164 0.000 0.172
#> TCGA-08-0352-01A-01 3 0.5582 -0.1147 0.012 0.452 0.492 0.000 0.044
#> TCGA-08-0360-01A-01 2 0.1965 0.7573 0.000 0.904 0.096 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.7708 0.2931 0.164 0.488 0.124 0.000 0.224
#> TCGA-08-0392-01A-01 5 0.3074 0.5746 0.000 0.196 0.000 0.000 0.804
#> TCGA-08-0509-01A-01 2 0.4302 0.1452 0.000 0.520 0.480 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.3561 0.4624 0.000 0.260 0.740 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.1270 0.7595 0.000 0.948 0.052 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0162 0.7496 0.000 0.996 0.000 0.000 0.004
#> TCGA-12-0619-01A-01 2 0.1908 0.7609 0.000 0.908 0.092 0.000 0.000
#> TCGA-12-0620-01A-01 5 0.4010 0.5788 0.000 0.056 0.160 0.000 0.784
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 6 0.4794 0.4971 0.328 0.000 0.060 0.004 0.000 0.608
#> TCGA-02-0010-01A-01 1 0.1485 0.6645 0.944 0.004 0.028 0.000 0.000 0.024
#> TCGA-02-0011-01B-01 6 0.4988 0.2306 0.380 0.004 0.064 0.000 0.000 0.552
#> TCGA-02-0014-01A-01 1 0.1789 0.6638 0.924 0.000 0.044 0.000 0.000 0.032
#> TCGA-02-0024-01B-01 1 0.2999 0.6770 0.836 0.000 0.040 0.000 0.000 0.124
#> TCGA-02-0026-01B-01 1 0.2000 0.6596 0.916 0.004 0.048 0.000 0.000 0.032
#> TCGA-02-0028-01A-01 1 0.1592 0.6636 0.940 0.008 0.032 0.000 0.000 0.020
#> TCGA-02-0046-01A-01 1 0.4767 0.4841 0.676 0.000 0.156 0.000 0.000 0.168
#> TCGA-02-0047-01A-01 6 0.2883 0.7047 0.060 0.008 0.068 0.000 0.000 0.864
#> TCGA-02-0048-01A-01 6 0.4480 0.4426 0.340 0.000 0.044 0.000 0.000 0.616
#> TCGA-02-0060-01A-01 6 0.1594 0.7070 0.052 0.000 0.016 0.000 0.000 0.932
#> TCGA-02-0069-01A-01 1 0.1737 0.6625 0.932 0.008 0.040 0.000 0.000 0.020
#> TCGA-02-0074-01A-01 1 0.3235 0.6080 0.824 0.008 0.136 0.000 0.000 0.032
#> TCGA-02-0080-01A-01 1 0.6400 0.3225 0.436 0.000 0.048 0.000 0.136 0.380
#> TCGA-02-0084-01A-03 2 0.6878 0.0370 0.020 0.360 0.016 0.000 0.332 0.272
#> TCGA-02-0087-01A-01 1 0.6582 0.4708 0.496 0.012 0.044 0.000 0.144 0.304
#> TCGA-02-0104-01A-01 5 0.5608 0.5995 0.120 0.000 0.080 0.012 0.684 0.104
#> TCGA-02-0114-01A-01 1 0.2571 0.6571 0.876 0.000 0.060 0.000 0.000 0.064
#> TCGA-02-0281-01A-01 1 0.3525 0.6382 0.840 0.008 0.072 0.000 0.036 0.044
#> TCGA-02-0321-01A-01 6 0.6516 -0.2300 0.004 0.380 0.028 0.000 0.184 0.404
#> TCGA-02-0325-01A-01 1 0.3802 0.5299 0.792 0.000 0.116 0.000 0.084 0.008
#> TCGA-02-0338-01A-01 1 0.1498 0.6660 0.940 0.000 0.028 0.000 0.000 0.032
#> TCGA-02-0339-01A-01 1 0.2822 0.6352 0.852 0.000 0.040 0.000 0.000 0.108
#> TCGA-02-0432-01A-02 6 0.6071 0.2293 0.280 0.000 0.040 0.000 0.136 0.544
#> TCGA-02-0439-01A-01 6 0.2745 0.6939 0.020 0.004 0.024 0.000 0.072 0.880
#> TCGA-02-0440-01A-01 1 0.4110 0.6427 0.712 0.000 0.052 0.000 0.000 0.236
#> TCGA-02-0446-01A-01 6 0.3663 0.6815 0.148 0.000 0.068 0.000 0.000 0.784
#> TCGA-06-0128-01A-01 6 0.4412 0.5820 0.256 0.008 0.048 0.000 0.000 0.688
#> TCGA-06-0129-01A-01 1 0.4368 0.3956 0.656 0.000 0.296 0.000 0.000 0.048
#> TCGA-06-0146-01A-01 1 0.3618 0.5362 0.808 0.000 0.104 0.000 0.080 0.008
#> TCGA-06-0156-01A-01 6 0.3351 0.6832 0.136 0.016 0.028 0.000 0.000 0.820
#> TCGA-06-0166-01A-01 6 0.3834 0.6762 0.140 0.044 0.024 0.000 0.000 0.792
#> TCGA-06-0174-01A-01 1 0.4587 0.5607 0.640 0.000 0.064 0.000 0.000 0.296
#> TCGA-06-0177-01A-01 1 0.5257 0.5936 0.624 0.000 0.052 0.000 0.044 0.280
#> TCGA-06-0238-01A-02 5 0.4506 0.6050 0.004 0.000 0.052 0.064 0.764 0.116
#> TCGA-06-0241-01A-02 6 0.4619 0.3448 0.348 0.000 0.052 0.000 0.000 0.600
#> TCGA-06-0410-01A-01 6 0.4921 0.3272 0.336 0.004 0.068 0.000 0.000 0.592
#> TCGA-06-0413-01A-01 1 0.1498 0.6660 0.940 0.000 0.028 0.000 0.000 0.032
#> TCGA-06-0414-01A-01 6 0.4694 0.3078 0.376 0.000 0.052 0.000 0.000 0.572
#> TCGA-06-0646-01A-01 2 0.5717 0.4522 0.024 0.528 0.100 0.000 0.000 0.348
#> TCGA-06-0648-01A-01 5 0.5616 0.5404 0.064 0.000 0.056 0.000 0.592 0.288
#> TCGA-08-0245-01A-01 1 0.3806 0.6591 0.752 0.000 0.048 0.000 0.000 0.200
#> TCGA-08-0344-01A-01 1 0.5191 0.5387 0.556 0.000 0.068 0.000 0.012 0.364
#> TCGA-08-0347-01A-01 6 0.1096 0.7072 0.020 0.004 0.008 0.000 0.004 0.964
#> TCGA-08-0348-01A-01 1 0.4809 0.5566 0.628 0.012 0.052 0.000 0.000 0.308
#> TCGA-08-0350-01A-01 5 0.7345 0.4092 0.116 0.020 0.132 0.000 0.440 0.292
#> TCGA-08-0353-01A-01 1 0.5296 0.5869 0.640 0.020 0.116 0.000 0.000 0.224
#> TCGA-08-0359-01A-01 6 0.1768 0.7008 0.044 0.000 0.012 0.008 0.004 0.932
#> TCGA-08-0385-01A-01 5 0.4600 0.6342 0.016 0.000 0.060 0.000 0.696 0.228
#> TCGA-08-0517-01A-01 6 0.3683 0.6405 0.184 0.000 0.048 0.000 0.000 0.768
#> TCGA-08-0524-01A-01 1 0.4620 0.6476 0.724 0.000 0.052 0.000 0.040 0.184
#> TCGA-12-0616-01A-01 5 0.6234 0.5335 0.120 0.004 0.072 0.000 0.580 0.224
#> TCGA-12-0618-01A-01 1 0.3385 0.6682 0.788 0.000 0.032 0.000 0.000 0.180
#> TCGA-02-0089-01A-01 6 0.3216 0.6931 0.020 0.060 0.072 0.000 0.000 0.848
#> TCGA-02-0113-01A-01 6 0.4388 0.6856 0.032 0.072 0.140 0.000 0.000 0.756
#> TCGA-02-0115-01A-01 4 0.5096 0.1321 0.044 0.000 0.016 0.480 0.000 0.460
#> TCGA-02-0451-01A-01 6 0.2515 0.7046 0.024 0.016 0.072 0.000 0.000 0.888
#> TCGA-06-0132-01A-02 4 0.1444 0.7925 0.000 0.000 0.000 0.928 0.000 0.072
#> TCGA-06-0133-01A-02 4 0.3470 0.7264 0.020 0.000 0.012 0.792 0.000 0.176
#> TCGA-06-0138-01A-02 6 0.2869 0.6599 0.008 0.008 0.012 0.004 0.104 0.864
#> TCGA-06-0160-01A-01 4 0.0000 0.7945 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0162-01A-01 6 0.6922 -0.1761 0.004 0.000 0.052 0.304 0.228 0.412
#> TCGA-06-0167-01A-01 4 0.0000 0.7945 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0171-01A-02 6 0.3635 0.6865 0.076 0.000 0.032 0.052 0.008 0.832
#> TCGA-06-0173-01A-01 6 0.3985 0.6904 0.136 0.016 0.068 0.000 0.000 0.780
#> TCGA-06-0179-01A-02 4 0.3079 0.7737 0.044 0.000 0.004 0.848 0.004 0.100
#> TCGA-06-0182-01A-01 6 0.6789 0.1943 0.040 0.296 0.004 0.004 0.204 0.452
#> TCGA-06-0185-01A-01 6 0.0820 0.7055 0.016 0.000 0.012 0.000 0.000 0.972
#> TCGA-06-0195-01B-01 4 0.2405 0.7612 0.000 0.000 0.016 0.880 0.004 0.100
#> TCGA-06-0208-01B-01 6 0.6335 0.4599 0.128 0.008 0.048 0.244 0.004 0.568
#> TCGA-06-0214-01A-02 6 0.4064 0.7010 0.120 0.028 0.068 0.000 0.000 0.784
#> TCGA-06-0219-01A-01 6 0.7328 -0.1568 0.024 0.000 0.052 0.272 0.256 0.396
#> TCGA-06-0221-01A-01 5 0.7004 -0.0492 0.004 0.004 0.036 0.292 0.344 0.320
#> TCGA-06-0237-01A-02 6 0.1363 0.7032 0.004 0.004 0.028 0.012 0.000 0.952
#> TCGA-06-0240-01A-02 4 0.0000 0.7945 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0349-01A-01 6 0.0964 0.7031 0.004 0.000 0.012 0.000 0.016 0.968
#> TCGA-08-0380-01A-01 6 0.3132 0.7048 0.008 0.032 0.064 0.000 0.032 0.864
#> TCGA-08-0386-01A-01 6 0.2152 0.7078 0.068 0.004 0.024 0.000 0.000 0.904
#> TCGA-08-0520-01A-01 6 0.3671 0.6032 0.004 0.008 0.028 0.004 0.160 0.796
#> TCGA-02-0007-01A-01 6 0.3352 0.6883 0.024 0.016 0.144 0.000 0.000 0.816
#> TCGA-02-0009-01A-01 3 0.4689 0.6477 0.196 0.000 0.712 0.000 0.060 0.032
#> TCGA-02-0016-01A-01 6 0.4426 0.6332 0.060 0.000 0.044 0.000 0.140 0.756
#> TCGA-02-0021-01A-01 3 0.4732 0.7234 0.156 0.072 0.728 0.000 0.000 0.044
#> TCGA-02-0023-01B-01 6 0.6558 0.1340 0.020 0.304 0.016 0.000 0.188 0.472
#> TCGA-02-0027-01A-01 3 0.5677 0.3454 0.384 0.012 0.508 0.000 0.008 0.088
#> TCGA-02-0038-01A-01 6 0.5029 0.5959 0.004 0.172 0.168 0.000 0.000 0.656
#> TCGA-02-0043-01A-01 1 0.4185 -0.2705 0.496 0.012 0.492 0.000 0.000 0.000
#> TCGA-02-0070-01A-01 2 0.5871 0.5406 0.008 0.564 0.108 0.000 0.024 0.296
#> TCGA-02-0102-01A-01 3 0.3683 0.7219 0.172 0.028 0.784 0.000 0.000 0.016
#> TCGA-02-0260-01A-03 1 0.4441 0.5589 0.740 0.004 0.036 0.000 0.184 0.036
#> TCGA-02-0269-01B-01 5 0.6600 0.2398 0.224 0.000 0.056 0.000 0.492 0.228
#> TCGA-02-0285-01A-01 2 0.5098 0.5728 0.000 0.608 0.100 0.000 0.004 0.288
#> TCGA-02-0289-01A-01 2 0.6208 0.4150 0.020 0.520 0.012 0.000 0.144 0.304
#> TCGA-02-0290-01A-01 5 0.3913 0.6517 0.004 0.032 0.088 0.000 0.808 0.068
#> TCGA-02-0317-01A-01 5 0.3610 0.6286 0.020 0.004 0.032 0.000 0.812 0.132
#> TCGA-02-0333-01A-02 1 0.6925 0.2040 0.380 0.004 0.044 0.000 0.312 0.260
#> TCGA-02-0422-01A-01 2 0.5363 0.5274 0.004 0.568 0.100 0.000 0.004 0.324
#> TCGA-02-0430-01A-01 1 0.6224 0.4560 0.580 0.080 0.140 0.000 0.000 0.200
#> TCGA-06-0125-01A-01 3 0.3314 0.6671 0.256 0.004 0.740 0.000 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.5530 0.6009 0.212 0.000 0.644 0.000 0.076 0.068
#> TCGA-06-0137-01A-03 6 0.5115 0.6384 0.092 0.000 0.128 0.000 0.072 0.708
#> TCGA-06-0145-01A-04 3 0.3759 0.6676 0.052 0.036 0.832 0.000 0.020 0.060
#> TCGA-06-0148-01A-01 2 0.5555 0.6012 0.032 0.656 0.172 0.000 0.008 0.132
#> TCGA-06-0187-01A-01 6 0.4795 0.5924 0.000 0.152 0.176 0.000 0.000 0.672
#> TCGA-06-0211-01B-01 6 0.2940 0.6839 0.112 0.004 0.036 0.000 0.000 0.848
#> TCGA-06-0402-01A-01 3 0.5004 0.5404 0.348 0.072 0.576 0.000 0.000 0.004
#> TCGA-08-0246-01A-01 2 0.4997 0.6166 0.004 0.640 0.088 0.000 0.004 0.264
#> TCGA-08-0354-01A-01 5 0.3524 0.6599 0.000 0.076 0.040 0.000 0.832 0.052
#> TCGA-08-0355-01A-01 2 0.6255 0.3053 0.012 0.472 0.020 0.000 0.132 0.364
#> TCGA-08-0357-01A-01 6 0.2727 0.6962 0.004 0.048 0.068 0.000 0.004 0.876
#> TCGA-08-0358-01A-01 5 0.2340 0.6443 0.012 0.012 0.044 0.012 0.912 0.008
#> TCGA-08-0375-01A-01 1 0.6204 0.5384 0.600 0.032 0.168 0.000 0.024 0.176
#> TCGA-08-0511-01A-01 6 0.2479 0.7068 0.008 0.012 0.064 0.000 0.020 0.896
#> TCGA-08-0514-01A-01 6 0.4322 0.6513 0.004 0.116 0.128 0.000 0.004 0.748
#> TCGA-08-0518-01A-01 3 0.3923 0.7190 0.192 0.060 0.748 0.000 0.000 0.000
#> TCGA-08-0529-01A-02 6 0.4841 0.5914 0.004 0.160 0.140 0.000 0.004 0.692
#> TCGA-08-0531-01A-01 6 0.3024 0.6854 0.004 0.028 0.120 0.000 0.004 0.844
#> TCGA-02-0057-01A-01 6 0.6037 0.4956 0.012 0.088 0.300 0.000 0.040 0.560
#> TCGA-02-0004-01A-01 2 0.2135 0.6896 0.000 0.872 0.000 0.000 0.128 0.000
#> TCGA-02-0006-01B-01 6 0.5369 0.5625 0.016 0.268 0.108 0.000 0.000 0.608
#> TCGA-02-0025-01A-01 5 0.4299 0.6369 0.000 0.100 0.072 0.000 0.776 0.052
#> TCGA-02-0033-01A-01 2 0.0405 0.7395 0.000 0.988 0.000 0.000 0.008 0.004
#> TCGA-02-0034-01A-01 2 0.1575 0.7512 0.000 0.936 0.032 0.000 0.000 0.032
#> TCGA-02-0039-01A-01 2 0.5213 0.5721 0.012 0.628 0.088 0.000 0.004 0.268
#> TCGA-02-0051-01A-01 5 0.3592 0.4487 0.000 0.344 0.000 0.000 0.656 0.000
#> TCGA-02-0054-01A-01 6 0.5604 0.5212 0.012 0.256 0.152 0.000 0.000 0.580
#> TCGA-02-0055-01A-01 2 0.2260 0.6820 0.000 0.860 0.000 0.000 0.140 0.000
#> TCGA-02-0059-01A-01 5 0.2454 0.6105 0.000 0.160 0.000 0.000 0.840 0.000
#> TCGA-02-0064-01A-01 3 0.4002 0.4900 0.000 0.320 0.660 0.000 0.000 0.020
#> TCGA-02-0075-01A-01 3 0.4303 0.5548 0.008 0.284 0.676 0.000 0.000 0.032
#> TCGA-02-0079-01A-03 5 0.2753 0.6417 0.012 0.080 0.004 0.000 0.876 0.028
#> TCGA-02-0085-01A-01 6 0.3021 0.6969 0.020 0.044 0.076 0.000 0.000 0.860
#> TCGA-02-0086-01A-01 2 0.1391 0.7527 0.000 0.944 0.016 0.000 0.000 0.040
#> TCGA-02-0099-01A-01 6 0.4992 0.5433 0.000 0.260 0.116 0.000 0.000 0.624
#> TCGA-02-0106-01A-01 2 0.0508 0.7379 0.000 0.984 0.000 0.000 0.012 0.004
#> TCGA-02-0107-01A-01 2 0.5245 0.2917 0.000 0.560 0.116 0.000 0.000 0.324
#> TCGA-02-0111-01A-01 2 0.3642 0.7048 0.000 0.800 0.016 0.000 0.144 0.040
#> TCGA-02-0326-01A-01 5 0.2306 0.6251 0.020 0.000 0.036 0.020 0.912 0.012
#> TCGA-02-0337-01A-01 2 0.4048 0.7208 0.004 0.788 0.088 0.000 0.016 0.104
#> TCGA-06-0122-01A-01 3 0.3341 0.7256 0.088 0.060 0.836 0.000 0.000 0.016
#> TCGA-06-0124-01A-01 3 0.4273 0.3071 0.000 0.380 0.596 0.000 0.000 0.024
#> TCGA-06-0130-01A-01 2 0.0551 0.7399 0.000 0.984 0.008 0.000 0.004 0.004
#> TCGA-06-0139-01A-01 2 0.0964 0.7461 0.000 0.968 0.004 0.000 0.012 0.016
#> TCGA-06-0143-01A-01 3 0.3473 0.7182 0.096 0.096 0.808 0.000 0.000 0.000
#> TCGA-06-0147-01A-01 2 0.2325 0.7497 0.000 0.892 0.060 0.000 0.000 0.048
#> TCGA-06-0149-01A-05 2 0.3296 0.7264 0.004 0.836 0.088 0.000 0.004 0.068
#> TCGA-06-0152-01A-02 5 0.4042 0.6585 0.012 0.020 0.056 0.000 0.796 0.116
#> TCGA-06-0154-01A-02 2 0.1789 0.7494 0.000 0.924 0.044 0.000 0.000 0.032
#> TCGA-06-0164-01A-01 2 0.1088 0.7458 0.000 0.960 0.016 0.000 0.000 0.024
#> TCGA-06-0175-01A-01 6 0.4088 0.7057 0.112 0.052 0.048 0.000 0.000 0.788
#> TCGA-06-0176-01A-03 2 0.1088 0.7391 0.000 0.960 0.000 0.000 0.024 0.016
#> TCGA-06-0184-01A-01 6 0.5342 0.4881 0.004 0.248 0.148 0.000 0.000 0.600
#> TCGA-06-0189-01A-05 2 0.3288 0.5421 0.000 0.724 0.000 0.000 0.276 0.000
#> TCGA-06-0190-01A-01 2 0.0291 0.7407 0.000 0.992 0.000 0.000 0.004 0.004
#> TCGA-06-0194-01A-01 2 0.0405 0.7429 0.000 0.988 0.000 0.000 0.004 0.008
#> TCGA-06-0197-01A-02 2 0.2340 0.6758 0.000 0.852 0.000 0.000 0.148 0.000
#> TCGA-06-0210-01A-01 2 0.1498 0.7538 0.000 0.940 0.028 0.000 0.000 0.032
#> TCGA-06-0397-01A-01 2 0.3854 0.6962 0.000 0.772 0.092 0.000 0.000 0.136
#> TCGA-06-0409-01A-02 2 0.2499 0.7437 0.000 0.880 0.072 0.000 0.000 0.048
#> TCGA-06-0412-01A-01 2 0.2277 0.7425 0.000 0.892 0.076 0.000 0.000 0.032
#> TCGA-06-0644-01A-02 2 0.2260 0.6820 0.000 0.860 0.000 0.000 0.140 0.000
#> TCGA-06-0645-01A-01 2 0.3458 0.7261 0.004 0.824 0.088 0.000 0.004 0.080
#> TCGA-08-0346-01A-01 2 0.4995 0.6997 0.004 0.728 0.088 0.000 0.112 0.068
#> TCGA-08-0352-01A-01 6 0.5811 -0.0366 0.012 0.388 0.084 0.000 0.016 0.500
#> TCGA-08-0360-01A-01 2 0.2277 0.7398 0.000 0.892 0.076 0.000 0.000 0.032
#> TCGA-08-0390-01A-01 2 0.6063 0.2985 0.004 0.452 0.000 0.000 0.244 0.300
#> TCGA-08-0392-01A-01 5 0.2340 0.6156 0.000 0.148 0.000 0.000 0.852 0.000
#> TCGA-08-0509-01A-01 2 0.5511 0.3087 0.004 0.532 0.128 0.000 0.000 0.336
#> TCGA-08-0510-01A-01 3 0.4425 0.5358 0.000 0.132 0.716 0.000 0.000 0.152
#> TCGA-08-0512-01A-01 2 0.2106 0.7462 0.000 0.904 0.064 0.000 0.000 0.032
#> TCGA-08-0522-01A-01 2 0.0692 0.7486 0.000 0.976 0.004 0.000 0.000 0.020
#> TCGA-12-0619-01A-01 2 0.3439 0.7171 0.000 0.808 0.072 0.000 0.000 0.120
#> TCGA-12-0620-01A-01 5 0.4118 0.6500 0.004 0.044 0.088 0.000 0.796 0.068
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> CV:mclust 160 5.17e-09 2
#> CV:mclust 143 2.26e-27 3
#> CV:mclust 147 9.18e-24 4
#> CV:mclust 116 1.54e-23 5
#> CV:mclust 135 4.29e-28 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "NMF"]
# you can also extract it by
# res = res_list["CV:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.815 0.883 0.953 0.4956 0.500 0.500
#> 3 3 0.579 0.707 0.860 0.3406 0.725 0.504
#> 4 4 0.607 0.702 0.819 0.1153 0.797 0.492
#> 5 5 0.742 0.742 0.859 0.0724 0.823 0.445
#> 6 6 0.750 0.669 0.828 0.0399 0.916 0.635
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.0672 0.9336 0.992 0.008
#> TCGA-02-0048-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0084-01A-03 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0087-01A-01 1 0.6623 0.7896 0.828 0.172
#> TCGA-02-0104-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0321-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0325-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.5059 0.8514 0.888 0.112
#> TCGA-02-0439-01A-01 1 0.7219 0.7551 0.800 0.200
#> TCGA-02-0440-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0128-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.2043 0.9174 0.968 0.032
#> TCGA-06-0166-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0174-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0177-01A-01 2 0.9209 0.4648 0.336 0.664
#> TCGA-06-0238-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0410-01A-01 2 0.4690 0.8619 0.100 0.900
#> TCGA-06-0413-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.9522 0.3851 0.372 0.628
#> TCGA-06-0648-01A-01 2 0.0376 0.9556 0.004 0.996
#> TCGA-08-0245-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-08-0344-01A-01 1 1.0000 0.0606 0.504 0.496
#> TCGA-08-0347-01A-01 2 0.0672 0.9522 0.008 0.992
#> TCGA-08-0348-01A-01 1 0.8207 0.6587 0.744 0.256
#> TCGA-08-0350-01A-01 2 0.1184 0.9453 0.016 0.984
#> TCGA-08-0353-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-08-0359-01A-01 2 0.9909 0.1611 0.444 0.556
#> TCGA-08-0385-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.1184 0.9282 0.984 0.016
#> TCGA-12-0616-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-12-0618-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.1843 0.9344 0.028 0.972
#> TCGA-02-0115-01A-01 1 0.0672 0.9337 0.992 0.008
#> TCGA-02-0451-01A-01 1 0.9795 0.3343 0.584 0.416
#> TCGA-06-0132-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0138-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.9795 0.3330 0.584 0.416
#> TCGA-06-0162-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0167-01A-01 2 0.9661 0.3199 0.392 0.608
#> TCGA-06-0171-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0173-01A-01 1 0.6973 0.7707 0.812 0.188
#> TCGA-06-0179-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0185-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0195-01B-01 2 0.3584 0.8949 0.068 0.932
#> TCGA-06-0208-01B-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0221-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0237-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0240-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0349-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-08-0520-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0007-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0009-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0016-01A-01 1 0.0672 0.9336 0.992 0.008
#> TCGA-02-0021-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0023-01B-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0038-01A-01 1 0.0376 0.9359 0.996 0.004
#> TCGA-02-0043-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0070-01A-01 2 0.9580 0.3534 0.380 0.620
#> TCGA-02-0102-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0260-01A-03 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0269-01B-01 2 0.9635 0.3295 0.388 0.612
#> TCGA-02-0285-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0289-01A-01 1 0.9393 0.4857 0.644 0.356
#> TCGA-02-0290-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0317-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0333-01A-02 1 0.9998 0.0820 0.508 0.492
#> TCGA-02-0422-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0430-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0125-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0126-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0137-01A-03 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0145-01A-04 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0148-01A-01 1 0.6048 0.8160 0.852 0.148
#> TCGA-06-0187-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0211-01B-01 2 0.9996 -0.0232 0.488 0.512
#> TCGA-06-0402-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-08-0246-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0357-01A-01 2 0.3584 0.8942 0.068 0.932
#> TCGA-08-0358-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0375-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-08-0511-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-08-0514-01A-01 1 0.6148 0.8119 0.848 0.152
#> TCGA-08-0518-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-08-0529-01A-02 1 0.3733 0.8859 0.928 0.072
#> TCGA-08-0531-01A-01 1 0.8861 0.5921 0.696 0.304
#> TCGA-02-0057-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0004-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.9323 0.4320 0.348 0.652
#> TCGA-02-0025-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0054-01A-01 1 0.5737 0.8287 0.864 0.136
#> TCGA-02-0055-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0064-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0075-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-02-0079-01A-03 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0099-01A-01 1 0.7602 0.7279 0.780 0.220
#> TCGA-02-0106-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-02-0337-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0122-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0124-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0143-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0175-01A-01 1 0.0376 0.9359 0.996 0.004
#> TCGA-06-0176-01A-03 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0397-01A-01 1 0.9754 0.3542 0.592 0.408
#> TCGA-06-0409-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.1184 0.9453 0.016 0.984
#> TCGA-06-0644-01A-02 2 0.0000 0.9588 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0510-01A-01 1 0.0000 0.9380 1.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9588 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.9588 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.4121 0.7585 0.832 0.000 0.168
#> TCGA-02-0010-01A-01 1 0.0237 0.8279 0.996 0.000 0.004
#> TCGA-02-0011-01B-01 1 0.3192 0.7911 0.888 0.000 0.112
#> TCGA-02-0014-01A-01 1 0.1031 0.8260 0.976 0.000 0.024
#> TCGA-02-0024-01B-01 1 0.5216 0.6781 0.740 0.000 0.260
#> TCGA-02-0026-01B-01 1 0.1411 0.8235 0.964 0.000 0.036
#> TCGA-02-0028-01A-01 1 0.0237 0.8278 0.996 0.004 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.8278 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 1 0.5098 0.6921 0.752 0.000 0.248
#> TCGA-02-0048-01A-01 1 0.1163 0.8252 0.972 0.000 0.028
#> TCGA-02-0060-01A-01 1 0.6180 0.4268 0.584 0.000 0.416
#> TCGA-02-0069-01A-01 1 0.0237 0.8278 0.996 0.004 0.000
#> TCGA-02-0074-01A-01 1 0.0424 0.8276 0.992 0.008 0.000
#> TCGA-02-0080-01A-01 1 0.5431 0.6512 0.716 0.000 0.284
#> TCGA-02-0084-01A-03 3 0.5859 0.4827 0.000 0.344 0.656
#> TCGA-02-0087-01A-01 1 0.5016 0.6999 0.760 0.000 0.240
#> TCGA-02-0104-01A-01 3 0.0424 0.8035 0.008 0.000 0.992
#> TCGA-02-0114-01A-01 1 0.0000 0.8278 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0892 0.8265 0.980 0.000 0.020
#> TCGA-02-0321-01A-01 3 0.4796 0.7112 0.000 0.220 0.780
#> TCGA-02-0325-01A-01 1 0.0424 0.8277 0.992 0.000 0.008
#> TCGA-02-0338-01A-01 1 0.0592 0.8276 0.988 0.000 0.012
#> TCGA-02-0339-01A-01 1 0.5216 0.6787 0.740 0.000 0.260
#> TCGA-02-0432-01A-02 1 0.6045 0.4977 0.620 0.000 0.380
#> TCGA-02-0439-01A-01 1 0.6286 0.3067 0.536 0.000 0.464
#> TCGA-02-0440-01A-01 1 0.1163 0.8245 0.972 0.000 0.028
#> TCGA-02-0446-01A-01 1 0.5254 0.6734 0.736 0.000 0.264
#> TCGA-06-0128-01A-01 1 0.0000 0.8278 1.000 0.000 0.000
#> TCGA-06-0129-01A-01 1 0.0424 0.8276 0.992 0.008 0.000
#> TCGA-06-0146-01A-01 1 0.4062 0.7595 0.836 0.000 0.164
#> TCGA-06-0156-01A-01 1 0.1289 0.8239 0.968 0.032 0.000
#> TCGA-06-0166-01A-01 3 0.5650 0.5960 0.000 0.312 0.688
#> TCGA-06-0174-01A-01 1 0.3941 0.7475 0.844 0.000 0.156
#> TCGA-06-0177-01A-01 3 0.3192 0.7284 0.112 0.000 0.888
#> TCGA-06-0238-01A-02 3 0.0424 0.8091 0.000 0.008 0.992
#> TCGA-06-0241-01A-02 1 0.2165 0.8103 0.936 0.000 0.064
#> TCGA-06-0410-01A-01 3 0.1643 0.7869 0.044 0.000 0.956
#> TCGA-06-0413-01A-01 1 0.0892 0.8266 0.980 0.000 0.020
#> TCGA-06-0414-01A-01 1 0.5706 0.5961 0.680 0.000 0.320
#> TCGA-06-0646-01A-01 1 0.7514 0.4448 0.616 0.328 0.056
#> TCGA-06-0648-01A-01 3 0.0747 0.8005 0.016 0.000 0.984
#> TCGA-08-0245-01A-01 1 0.0237 0.8281 0.996 0.000 0.004
#> TCGA-08-0344-01A-01 3 0.4452 0.6215 0.192 0.000 0.808
#> TCGA-08-0347-01A-01 3 0.0747 0.8006 0.016 0.000 0.984
#> TCGA-08-0348-01A-01 3 0.5810 0.3866 0.336 0.000 0.664
#> TCGA-08-0350-01A-01 3 0.3607 0.7883 0.008 0.112 0.880
#> TCGA-08-0353-01A-01 1 0.0424 0.8276 0.992 0.008 0.000
#> TCGA-08-0359-01A-01 3 0.3192 0.7275 0.112 0.000 0.888
#> TCGA-08-0385-01A-01 3 0.1267 0.8121 0.004 0.024 0.972
#> TCGA-08-0517-01A-01 1 0.0000 0.8278 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 3 0.6267 -0.0576 0.452 0.000 0.548
#> TCGA-12-0616-01A-01 3 0.4555 0.7275 0.000 0.200 0.800
#> TCGA-12-0618-01A-01 1 0.6305 0.2463 0.516 0.000 0.484
#> TCGA-02-0089-01A-01 2 0.5859 0.4682 0.000 0.656 0.344
#> TCGA-02-0113-01A-01 2 0.1031 0.8569 0.024 0.976 0.000
#> TCGA-02-0115-01A-01 1 0.9111 0.5218 0.548 0.240 0.212
#> TCGA-02-0451-01A-01 2 0.9585 0.0554 0.332 0.456 0.212
#> TCGA-06-0132-01A-02 3 0.0237 0.8052 0.004 0.000 0.996
#> TCGA-06-0133-01A-02 3 0.0000 0.8065 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 3 0.4178 0.7488 0.000 0.172 0.828
#> TCGA-06-0160-01A-01 3 0.3116 0.7317 0.108 0.000 0.892
#> TCGA-06-0162-01A-01 3 0.1163 0.8116 0.000 0.028 0.972
#> TCGA-06-0167-01A-01 3 0.2356 0.7638 0.072 0.000 0.928
#> TCGA-06-0171-01A-02 3 0.1031 0.8121 0.000 0.024 0.976
#> TCGA-06-0173-01A-01 1 0.1647 0.8229 0.960 0.036 0.004
#> TCGA-06-0179-01A-02 3 0.0424 0.8035 0.008 0.000 0.992
#> TCGA-06-0182-01A-01 3 0.5178 0.6724 0.000 0.256 0.744
#> TCGA-06-0185-01A-01 3 0.0237 0.8079 0.000 0.004 0.996
#> TCGA-06-0195-01B-01 3 0.1860 0.7782 0.052 0.000 0.948
#> TCGA-06-0208-01B-01 3 0.0237 0.8079 0.000 0.004 0.996
#> TCGA-06-0214-01A-02 2 0.6252 0.0448 0.000 0.556 0.444
#> TCGA-06-0219-01A-01 3 0.2711 0.7970 0.000 0.088 0.912
#> TCGA-06-0221-01A-01 3 0.0237 0.8079 0.000 0.004 0.996
#> TCGA-06-0237-01A-02 3 0.1964 0.8078 0.000 0.056 0.944
#> TCGA-06-0240-01A-02 3 0.0237 0.8052 0.004 0.000 0.996
#> TCGA-08-0349-01A-01 3 0.0237 0.8079 0.000 0.004 0.996
#> TCGA-08-0380-01A-01 3 0.5138 0.6821 0.000 0.252 0.748
#> TCGA-08-0386-01A-01 1 0.4062 0.7589 0.836 0.000 0.164
#> TCGA-08-0520-01A-01 3 0.4555 0.7280 0.000 0.200 0.800
#> TCGA-02-0007-01A-01 1 0.0424 0.8276 0.992 0.008 0.000
#> TCGA-02-0009-01A-01 1 0.1163 0.8226 0.972 0.028 0.000
#> TCGA-02-0016-01A-01 1 0.5216 0.6794 0.740 0.000 0.260
#> TCGA-02-0021-01A-01 1 0.1860 0.8127 0.948 0.052 0.000
#> TCGA-02-0023-01B-01 3 0.1031 0.8116 0.000 0.024 0.976
#> TCGA-02-0027-01A-01 1 0.0424 0.8276 0.992 0.008 0.000
#> TCGA-02-0038-01A-01 2 0.6295 0.1094 0.472 0.528 0.000
#> TCGA-02-0043-01A-01 1 0.1411 0.8197 0.964 0.036 0.000
#> TCGA-02-0070-01A-01 2 0.0747 0.8604 0.016 0.984 0.000
#> TCGA-02-0102-01A-01 1 0.1529 0.8181 0.960 0.040 0.000
#> TCGA-02-0260-01A-03 1 0.0237 0.8278 0.996 0.004 0.000
#> TCGA-02-0269-01B-01 3 0.9007 0.5057 0.268 0.180 0.552
#> TCGA-02-0285-01A-01 2 0.1031 0.8607 0.000 0.976 0.024
#> TCGA-02-0289-01A-01 1 0.6853 0.6267 0.712 0.224 0.064
#> TCGA-02-0290-01A-01 3 0.6235 0.3468 0.000 0.436 0.564
#> TCGA-02-0317-01A-01 3 0.5098 0.6813 0.000 0.248 0.752
#> TCGA-02-0333-01A-02 1 0.8393 0.2429 0.516 0.088 0.396
#> TCGA-02-0422-01A-01 2 0.4452 0.6893 0.000 0.808 0.192
#> TCGA-02-0430-01A-01 1 0.2261 0.8069 0.932 0.068 0.000
#> TCGA-06-0125-01A-01 1 0.1031 0.8239 0.976 0.024 0.000
#> TCGA-06-0126-01A-01 1 0.0424 0.8276 0.992 0.008 0.000
#> TCGA-06-0137-01A-03 1 0.2066 0.8154 0.940 0.000 0.060
#> TCGA-06-0145-01A-04 1 0.5497 0.5345 0.708 0.292 0.000
#> TCGA-06-0148-01A-01 2 0.1964 0.8374 0.056 0.944 0.000
#> TCGA-06-0187-01A-01 2 0.6026 0.3928 0.376 0.624 0.000
#> TCGA-06-0211-01B-01 3 0.6189 0.2514 0.364 0.004 0.632
#> TCGA-06-0402-01A-01 1 0.1529 0.8181 0.960 0.040 0.000
#> TCGA-08-0246-01A-01 2 0.1289 0.8565 0.000 0.968 0.032
#> TCGA-08-0354-01A-01 3 0.6008 0.4928 0.000 0.372 0.628
#> TCGA-08-0355-01A-01 3 0.5621 0.6130 0.000 0.308 0.692
#> TCGA-08-0357-01A-01 3 0.5965 0.7593 0.100 0.108 0.792
#> TCGA-08-0358-01A-01 3 0.4796 0.7109 0.000 0.220 0.780
#> TCGA-08-0375-01A-01 1 0.0592 0.8280 0.988 0.012 0.000
#> TCGA-08-0511-01A-01 1 0.6098 0.7437 0.768 0.056 0.176
#> TCGA-08-0514-01A-01 2 0.4062 0.7427 0.164 0.836 0.000
#> TCGA-08-0518-01A-01 1 0.1753 0.8143 0.952 0.048 0.000
#> TCGA-08-0529-01A-02 1 0.6308 0.0605 0.508 0.492 0.000
#> TCGA-08-0531-01A-01 1 0.5541 0.6501 0.740 0.252 0.008
#> TCGA-02-0057-01A-01 1 0.6309 -0.0541 0.500 0.500 0.000
#> TCGA-02-0004-01A-01 2 0.0747 0.8633 0.000 0.984 0.016
#> TCGA-02-0006-01B-01 2 0.1860 0.8394 0.052 0.948 0.000
#> TCGA-02-0025-01A-01 2 0.2537 0.8216 0.000 0.920 0.080
#> TCGA-02-0033-01A-01 2 0.0000 0.8657 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0237 0.8643 0.004 0.996 0.000
#> TCGA-02-0039-01A-01 2 0.1643 0.8509 0.000 0.956 0.044
#> TCGA-02-0051-01A-01 2 0.3482 0.7719 0.000 0.872 0.128
#> TCGA-02-0054-01A-01 2 0.3116 0.7968 0.108 0.892 0.000
#> TCGA-02-0055-01A-01 2 0.2066 0.8381 0.000 0.940 0.060
#> TCGA-02-0059-01A-01 2 0.5178 0.5750 0.000 0.744 0.256
#> TCGA-02-0064-01A-01 2 0.4842 0.6712 0.224 0.776 0.000
#> TCGA-02-0075-01A-01 2 0.5968 0.4291 0.364 0.636 0.000
#> TCGA-02-0079-01A-03 2 0.5882 0.3668 0.000 0.652 0.348
#> TCGA-02-0085-01A-01 2 0.5968 0.4350 0.000 0.636 0.364
#> TCGA-02-0086-01A-01 2 0.0237 0.8659 0.000 0.996 0.004
#> TCGA-02-0099-01A-01 2 0.1411 0.8502 0.036 0.964 0.000
#> TCGA-02-0106-01A-01 2 0.0000 0.8657 0.000 1.000 0.000
#> TCGA-02-0107-01A-01 2 0.0424 0.8655 0.000 0.992 0.008
#> TCGA-02-0111-01A-01 2 0.2261 0.8319 0.000 0.932 0.068
#> TCGA-02-0326-01A-01 3 0.2625 0.7990 0.000 0.084 0.916
#> TCGA-02-0337-01A-01 2 0.1643 0.8494 0.000 0.956 0.044
#> TCGA-06-0122-01A-01 1 0.5591 0.5105 0.696 0.304 0.000
#> TCGA-06-0124-01A-01 2 0.5327 0.6022 0.272 0.728 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.8657 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0424 0.8655 0.000 0.992 0.008
#> TCGA-06-0143-01A-01 1 0.6026 0.3494 0.624 0.376 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.8657 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 2 0.0424 0.8655 0.000 0.992 0.008
#> TCGA-06-0152-01A-02 3 0.5948 0.5168 0.000 0.360 0.640
#> TCGA-06-0154-01A-02 2 0.0000 0.8657 0.000 1.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.8657 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 1 0.6274 0.1129 0.544 0.456 0.000
#> TCGA-06-0176-01A-03 2 0.0237 0.8659 0.000 0.996 0.004
#> TCGA-06-0184-01A-01 2 0.1163 0.8586 0.000 0.972 0.028
#> TCGA-06-0189-01A-05 2 0.4605 0.6676 0.000 0.796 0.204
#> TCGA-06-0190-01A-01 2 0.0424 0.8655 0.000 0.992 0.008
#> TCGA-06-0194-01A-01 2 0.0424 0.8655 0.000 0.992 0.008
#> TCGA-06-0197-01A-02 2 0.1860 0.8438 0.000 0.948 0.052
#> TCGA-06-0210-01A-01 2 0.0424 0.8655 0.000 0.992 0.008
#> TCGA-06-0397-01A-01 2 0.0892 0.8580 0.020 0.980 0.000
#> TCGA-06-0409-01A-02 2 0.0237 0.8659 0.000 0.996 0.004
#> TCGA-06-0412-01A-01 2 0.0592 0.8615 0.012 0.988 0.000
#> TCGA-06-0644-01A-02 2 0.0747 0.8633 0.000 0.984 0.016
#> TCGA-06-0645-01A-01 2 0.1163 0.8585 0.000 0.972 0.028
#> TCGA-08-0346-01A-01 2 0.1031 0.8603 0.000 0.976 0.024
#> TCGA-08-0352-01A-01 2 0.4834 0.6693 0.004 0.792 0.204
#> TCGA-08-0360-01A-01 2 0.0237 0.8659 0.000 0.996 0.004
#> TCGA-08-0390-01A-01 3 0.5497 0.6318 0.000 0.292 0.708
#> TCGA-08-0392-01A-01 3 0.6291 0.2565 0.000 0.468 0.532
#> TCGA-08-0509-01A-01 2 0.0237 0.8659 0.000 0.996 0.004
#> TCGA-08-0510-01A-01 2 0.5760 0.5040 0.328 0.672 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.8657 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8657 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.8657 0.000 1.000 0.000
#> TCGA-12-0620-01A-01 2 0.5621 0.4661 0.000 0.692 0.308
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 4 0.4250 0.6443 0.276 0.000 0.000 0.724
#> TCGA-02-0010-01A-01 1 0.0707 0.8027 0.980 0.000 0.000 0.020
#> TCGA-02-0011-01B-01 1 0.2081 0.7938 0.916 0.000 0.000 0.084
#> TCGA-02-0014-01A-01 1 0.1118 0.7980 0.964 0.000 0.000 0.036
#> TCGA-02-0024-01B-01 1 0.3907 0.6460 0.768 0.000 0.000 0.232
#> TCGA-02-0026-01B-01 1 0.0707 0.8028 0.980 0.000 0.000 0.020
#> TCGA-02-0028-01A-01 1 0.0592 0.8035 0.984 0.000 0.000 0.016
#> TCGA-02-0046-01A-01 1 0.0895 0.8034 0.976 0.004 0.000 0.020
#> TCGA-02-0047-01A-01 4 0.2983 0.7567 0.108 0.004 0.008 0.880
#> TCGA-02-0048-01A-01 1 0.1398 0.8012 0.956 0.004 0.000 0.040
#> TCGA-02-0060-01A-01 4 0.3877 0.7641 0.112 0.000 0.048 0.840
#> TCGA-02-0069-01A-01 1 0.0592 0.8035 0.984 0.000 0.000 0.016
#> TCGA-02-0074-01A-01 1 0.0779 0.8039 0.980 0.004 0.000 0.016
#> TCGA-02-0080-01A-01 1 0.5031 0.7477 0.740 0.000 0.048 0.212
#> TCGA-02-0084-01A-03 3 0.4760 0.7258 0.004 0.052 0.784 0.160
#> TCGA-02-0087-01A-01 1 0.6109 0.7227 0.692 0.004 0.132 0.172
#> TCGA-02-0104-01A-01 3 0.3534 0.6779 0.008 0.004 0.840 0.148
#> TCGA-02-0114-01A-01 1 0.1302 0.7949 0.956 0.000 0.000 0.044
#> TCGA-02-0281-01A-01 1 0.0469 0.8043 0.988 0.000 0.000 0.012
#> TCGA-02-0321-01A-01 3 0.1637 0.7819 0.000 0.060 0.940 0.000
#> TCGA-02-0325-01A-01 1 0.4739 0.7772 0.796 0.008 0.056 0.140
#> TCGA-02-0338-01A-01 1 0.1118 0.7980 0.964 0.000 0.000 0.036
#> TCGA-02-0339-01A-01 1 0.2011 0.7928 0.920 0.000 0.000 0.080
#> TCGA-02-0432-01A-02 1 0.5906 0.5125 0.644 0.000 0.064 0.292
#> TCGA-02-0439-01A-01 4 0.6300 0.2732 0.308 0.000 0.084 0.608
#> TCGA-02-0440-01A-01 1 0.1474 0.7912 0.948 0.000 0.000 0.052
#> TCGA-02-0446-01A-01 4 0.3680 0.7352 0.160 0.004 0.008 0.828
#> TCGA-06-0128-01A-01 4 0.6101 0.3570 0.404 0.028 0.012 0.556
#> TCGA-06-0129-01A-01 1 0.1394 0.8076 0.964 0.008 0.016 0.012
#> TCGA-06-0146-01A-01 1 0.2124 0.8018 0.924 0.000 0.008 0.068
#> TCGA-06-0156-01A-01 1 0.7585 0.0124 0.472 0.224 0.000 0.304
#> TCGA-06-0166-01A-01 3 0.8192 0.5355 0.228 0.120 0.560 0.092
#> TCGA-06-0174-01A-01 1 0.2081 0.7727 0.916 0.000 0.000 0.084
#> TCGA-06-0177-01A-01 3 0.6116 0.4589 0.320 0.000 0.612 0.068
#> TCGA-06-0238-01A-02 3 0.2111 0.7596 0.000 0.024 0.932 0.044
#> TCGA-06-0241-01A-02 1 0.2814 0.7319 0.868 0.000 0.000 0.132
#> TCGA-06-0410-01A-01 3 0.7811 -0.0506 0.268 0.000 0.412 0.320
#> TCGA-06-0413-01A-01 1 0.1022 0.7995 0.968 0.000 0.000 0.032
#> TCGA-06-0414-01A-01 4 0.4713 0.5243 0.360 0.000 0.000 0.640
#> TCGA-06-0646-01A-01 1 0.6354 0.6563 0.700 0.164 0.112 0.024
#> TCGA-06-0648-01A-01 3 0.2670 0.7330 0.040 0.000 0.908 0.052
#> TCGA-08-0245-01A-01 1 0.1004 0.8016 0.972 0.004 0.000 0.024
#> TCGA-08-0344-01A-01 1 0.7585 0.1860 0.472 0.000 0.304 0.224
#> TCGA-08-0347-01A-01 4 0.4012 0.7668 0.016 0.000 0.184 0.800
#> TCGA-08-0348-01A-01 1 0.3485 0.7431 0.856 0.000 0.116 0.028
#> TCGA-08-0350-01A-01 3 0.2573 0.7804 0.024 0.044 0.920 0.012
#> TCGA-08-0353-01A-01 1 0.0657 0.8072 0.984 0.004 0.000 0.012
#> TCGA-08-0359-01A-01 4 0.3647 0.7851 0.040 0.000 0.108 0.852
#> TCGA-08-0385-01A-01 3 0.1994 0.7808 0.008 0.052 0.936 0.004
#> TCGA-08-0517-01A-01 1 0.1305 0.7996 0.960 0.004 0.000 0.036
#> TCGA-08-0524-01A-01 1 0.3372 0.7492 0.868 0.000 0.096 0.036
#> TCGA-12-0616-01A-01 3 0.1970 0.7830 0.008 0.060 0.932 0.000
#> TCGA-12-0618-01A-01 1 0.2522 0.7824 0.908 0.000 0.016 0.076
#> TCGA-02-0089-01A-01 4 0.3229 0.7263 0.000 0.072 0.048 0.880
#> TCGA-02-0113-01A-01 2 0.3217 0.8109 0.000 0.860 0.012 0.128
#> TCGA-02-0115-01A-01 4 0.2115 0.7468 0.024 0.036 0.004 0.936
#> TCGA-02-0451-01A-01 4 0.2528 0.7357 0.008 0.080 0.004 0.908
#> TCGA-06-0132-01A-02 4 0.2973 0.7778 0.000 0.000 0.144 0.856
#> TCGA-06-0133-01A-02 4 0.2973 0.7768 0.000 0.000 0.144 0.856
#> TCGA-06-0138-01A-02 3 0.5678 0.3130 0.000 0.044 0.640 0.316
#> TCGA-06-0160-01A-01 4 0.3634 0.7843 0.048 0.000 0.096 0.856
#> TCGA-06-0162-01A-01 4 0.5290 0.4901 0.000 0.012 0.404 0.584
#> TCGA-06-0167-01A-01 4 0.3612 0.7847 0.044 0.000 0.100 0.856
#> TCGA-06-0171-01A-02 4 0.5169 0.6640 0.000 0.032 0.272 0.696
#> TCGA-06-0173-01A-01 4 0.5906 0.6667 0.188 0.104 0.004 0.704
#> TCGA-06-0179-01A-02 4 0.3325 0.7848 0.024 0.000 0.112 0.864
#> TCGA-06-0182-01A-01 3 0.4599 0.7194 0.000 0.088 0.800 0.112
#> TCGA-06-0185-01A-01 4 0.3710 0.7574 0.000 0.004 0.192 0.804
#> TCGA-06-0195-01B-01 4 0.3652 0.7835 0.052 0.000 0.092 0.856
#> TCGA-06-0208-01B-01 4 0.3538 0.7746 0.004 0.004 0.160 0.832
#> TCGA-06-0214-01A-02 2 0.6147 -0.0282 0.000 0.488 0.048 0.464
#> TCGA-06-0219-01A-01 4 0.6011 0.2267 0.000 0.040 0.476 0.484
#> TCGA-06-0221-01A-01 4 0.4431 0.6653 0.000 0.000 0.304 0.696
#> TCGA-06-0237-01A-02 4 0.6005 0.2642 0.000 0.040 0.460 0.500
#> TCGA-06-0240-01A-02 4 0.3219 0.7718 0.000 0.000 0.164 0.836
#> TCGA-08-0349-01A-01 4 0.4992 0.3484 0.000 0.000 0.476 0.524
#> TCGA-08-0380-01A-01 4 0.5122 0.7255 0.000 0.080 0.164 0.756
#> TCGA-08-0386-01A-01 1 0.4034 0.7727 0.804 0.004 0.012 0.180
#> TCGA-08-0520-01A-01 3 0.2919 0.7563 0.000 0.044 0.896 0.060
#> TCGA-02-0007-01A-01 1 0.4963 0.7780 0.796 0.024 0.052 0.128
#> TCGA-02-0009-01A-01 1 0.5292 0.7676 0.776 0.028 0.056 0.140
#> TCGA-02-0016-01A-01 1 0.5359 0.7063 0.680 0.004 0.028 0.288
#> TCGA-02-0021-01A-01 1 0.5092 0.7731 0.788 0.024 0.056 0.132
#> TCGA-02-0023-01B-01 3 0.2654 0.7041 0.000 0.004 0.888 0.108
#> TCGA-02-0027-01A-01 1 0.4660 0.7839 0.816 0.020 0.056 0.108
#> TCGA-02-0038-01A-01 2 0.6095 0.6951 0.060 0.732 0.056 0.152
#> TCGA-02-0043-01A-01 1 0.3122 0.7998 0.888 0.012 0.016 0.084
#> TCGA-02-0070-01A-01 3 0.9078 0.4483 0.224 0.200 0.464 0.112
#> TCGA-02-0102-01A-01 1 0.5242 0.7693 0.780 0.028 0.056 0.136
#> TCGA-02-0260-01A-03 1 0.4963 0.7801 0.792 0.012 0.076 0.120
#> TCGA-02-0269-01B-01 3 0.4725 0.6734 0.076 0.008 0.804 0.112
#> TCGA-02-0285-01A-01 3 0.5239 0.7419 0.004 0.128 0.764 0.104
#> TCGA-02-0289-01A-01 1 0.8102 0.4027 0.480 0.040 0.340 0.140
#> TCGA-02-0290-01A-01 3 0.2216 0.7827 0.000 0.092 0.908 0.000
#> TCGA-02-0317-01A-01 3 0.3312 0.7675 0.004 0.040 0.880 0.076
#> TCGA-02-0333-01A-02 3 0.6685 0.4983 0.200 0.008 0.644 0.148
#> TCGA-02-0422-01A-01 3 0.5443 0.7483 0.024 0.108 0.772 0.096
#> TCGA-02-0430-01A-01 1 0.3623 0.7937 0.856 0.012 0.016 0.116
#> TCGA-06-0125-01A-01 1 0.5092 0.7729 0.788 0.024 0.056 0.132
#> TCGA-06-0126-01A-01 1 0.5194 0.7702 0.780 0.024 0.056 0.140
#> TCGA-06-0137-01A-03 1 0.6376 0.6657 0.624 0.016 0.056 0.304
#> TCGA-06-0145-01A-04 1 0.8478 0.1998 0.428 0.368 0.056 0.148
#> TCGA-06-0148-01A-01 1 0.8107 0.6343 0.592 0.136 0.144 0.128
#> TCGA-06-0187-01A-01 2 0.7645 0.5153 0.192 0.608 0.056 0.144
#> TCGA-06-0211-01B-01 1 0.7018 0.2008 0.492 0.004 0.400 0.104
#> TCGA-06-0402-01A-01 1 0.1953 0.8069 0.940 0.012 0.004 0.044
#> TCGA-08-0246-01A-01 2 0.6514 0.0652 0.000 0.516 0.408 0.076
#> TCGA-08-0354-01A-01 3 0.2011 0.7833 0.000 0.080 0.920 0.000
#> TCGA-08-0355-01A-01 3 0.3652 0.7708 0.000 0.052 0.856 0.092
#> TCGA-08-0357-01A-01 3 0.7370 0.5444 0.240 0.052 0.612 0.096
#> TCGA-08-0358-01A-01 3 0.1722 0.7783 0.000 0.048 0.944 0.008
#> TCGA-08-0375-01A-01 1 0.4570 0.7866 0.812 0.008 0.064 0.116
#> TCGA-08-0511-01A-01 1 0.7174 0.6123 0.576 0.088 0.028 0.308
#> TCGA-08-0514-01A-01 2 0.8887 0.2051 0.284 0.464 0.104 0.148
#> TCGA-08-0518-01A-01 1 0.5292 0.7676 0.776 0.028 0.056 0.140
#> TCGA-08-0529-01A-02 1 0.7077 0.7037 0.672 0.104 0.076 0.148
#> TCGA-08-0531-01A-01 1 0.7691 0.5812 0.572 0.036 0.244 0.148
#> TCGA-02-0057-01A-01 2 0.5664 0.7120 0.036 0.752 0.056 0.156
#> TCGA-02-0004-01A-01 2 0.1557 0.8481 0.000 0.944 0.056 0.000
#> TCGA-02-0006-01B-01 2 0.1486 0.8550 0.008 0.960 0.008 0.024
#> TCGA-02-0025-01A-01 3 0.4164 0.6876 0.000 0.264 0.736 0.000
#> TCGA-02-0033-01A-01 2 0.0707 0.8617 0.000 0.980 0.020 0.000
#> TCGA-02-0034-01A-01 2 0.0707 0.8617 0.000 0.980 0.020 0.000
#> TCGA-02-0039-01A-01 2 0.2730 0.8247 0.000 0.896 0.088 0.016
#> TCGA-02-0051-01A-01 3 0.4888 0.4347 0.000 0.412 0.588 0.000
#> TCGA-02-0054-01A-01 2 0.2010 0.8414 0.008 0.940 0.012 0.040
#> TCGA-02-0055-01A-01 2 0.1637 0.8455 0.000 0.940 0.060 0.000
#> TCGA-02-0059-01A-01 3 0.3975 0.7080 0.000 0.240 0.760 0.000
#> TCGA-02-0064-01A-01 2 0.2652 0.8204 0.004 0.912 0.056 0.028
#> TCGA-02-0075-01A-01 2 0.3210 0.8157 0.024 0.896 0.044 0.036
#> TCGA-02-0079-01A-03 3 0.2976 0.7780 0.000 0.120 0.872 0.008
#> TCGA-02-0085-01A-01 4 0.4149 0.6802 0.000 0.168 0.028 0.804
#> TCGA-02-0086-01A-01 2 0.0707 0.8621 0.000 0.980 0.020 0.000
#> TCGA-02-0099-01A-01 2 0.1151 0.8571 0.000 0.968 0.008 0.024
#> TCGA-02-0106-01A-01 2 0.1389 0.8540 0.000 0.952 0.048 0.000
#> TCGA-02-0107-01A-01 2 0.0469 0.8616 0.000 0.988 0.012 0.000
#> TCGA-02-0111-01A-01 2 0.2281 0.8196 0.000 0.904 0.096 0.000
#> TCGA-02-0326-01A-01 3 0.2214 0.7613 0.000 0.028 0.928 0.044
#> TCGA-02-0337-01A-01 2 0.4830 0.3021 0.000 0.608 0.392 0.000
#> TCGA-06-0122-01A-01 2 0.7141 0.6023 0.144 0.660 0.056 0.140
#> TCGA-06-0124-01A-01 2 0.3791 0.7913 0.008 0.860 0.056 0.076
#> TCGA-06-0130-01A-01 2 0.0707 0.8617 0.000 0.980 0.020 0.000
#> TCGA-06-0139-01A-01 2 0.0817 0.8612 0.000 0.976 0.024 0.000
#> TCGA-06-0143-01A-01 2 0.6817 0.6378 0.128 0.688 0.056 0.128
#> TCGA-06-0147-01A-01 2 0.0707 0.8564 0.000 0.980 0.020 0.000
#> TCGA-06-0149-01A-05 2 0.4227 0.7775 0.000 0.820 0.060 0.120
#> TCGA-06-0152-01A-02 3 0.1978 0.7837 0.000 0.068 0.928 0.004
#> TCGA-06-0154-01A-02 2 0.0921 0.8602 0.000 0.972 0.028 0.000
#> TCGA-06-0164-01A-01 2 0.0592 0.8618 0.000 0.984 0.016 0.000
#> TCGA-06-0175-01A-01 2 0.4199 0.7828 0.096 0.836 0.008 0.060
#> TCGA-06-0176-01A-03 2 0.1118 0.8579 0.000 0.964 0.036 0.000
#> TCGA-06-0184-01A-01 2 0.2411 0.8460 0.000 0.920 0.040 0.040
#> TCGA-06-0189-01A-05 3 0.4866 0.4410 0.000 0.404 0.596 0.000
#> TCGA-06-0190-01A-01 2 0.0817 0.8612 0.000 0.976 0.024 0.000
#> TCGA-06-0194-01A-01 2 0.1118 0.8579 0.000 0.964 0.036 0.000
#> TCGA-06-0197-01A-02 2 0.1637 0.8455 0.000 0.940 0.060 0.000
#> TCGA-06-0210-01A-01 2 0.1211 0.8565 0.000 0.960 0.040 0.000
#> TCGA-06-0397-01A-01 2 0.1109 0.8614 0.004 0.968 0.028 0.000
#> TCGA-06-0409-01A-02 2 0.0469 0.8616 0.000 0.988 0.012 0.000
#> TCGA-06-0412-01A-01 2 0.0657 0.8622 0.000 0.984 0.012 0.004
#> TCGA-06-0644-01A-02 2 0.1716 0.8428 0.000 0.936 0.064 0.000
#> TCGA-06-0645-01A-01 2 0.1211 0.8579 0.000 0.960 0.040 0.000
#> TCGA-08-0346-01A-01 2 0.4746 0.3269 0.000 0.632 0.368 0.000
#> TCGA-08-0352-01A-01 2 0.5497 0.6273 0.000 0.672 0.044 0.284
#> TCGA-08-0360-01A-01 2 0.0707 0.8617 0.000 0.980 0.020 0.000
#> TCGA-08-0390-01A-01 3 0.3763 0.7638 0.000 0.144 0.832 0.024
#> TCGA-08-0392-01A-01 3 0.3266 0.7557 0.000 0.168 0.832 0.000
#> TCGA-08-0509-01A-01 2 0.0524 0.8593 0.000 0.988 0.008 0.004
#> TCGA-08-0510-01A-01 2 0.5217 0.7418 0.036 0.788 0.056 0.120
#> TCGA-08-0512-01A-01 2 0.0592 0.8618 0.000 0.984 0.016 0.000
#> TCGA-08-0522-01A-01 2 0.0817 0.8612 0.000 0.976 0.024 0.000
#> TCGA-12-0619-01A-01 2 0.1211 0.8570 0.000 0.960 0.040 0.000
#> TCGA-12-0620-01A-01 3 0.2814 0.7731 0.000 0.132 0.868 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.2470 0.85573 0.884 0.000 0.012 0.104 0.000
#> TCGA-02-0010-01A-01 1 0.1043 0.90958 0.960 0.000 0.040 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.2331 0.88164 0.900 0.000 0.080 0.020 0.000
#> TCGA-02-0014-01A-01 1 0.0794 0.91057 0.972 0.000 0.028 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.1117 0.90775 0.964 0.000 0.016 0.020 0.000
#> TCGA-02-0026-01B-01 1 0.1197 0.90847 0.952 0.000 0.048 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.1043 0.91014 0.960 0.000 0.040 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.1043 0.91034 0.960 0.000 0.040 0.000 0.000
#> TCGA-02-0047-01A-01 4 0.0324 0.80787 0.004 0.000 0.004 0.992 0.000
#> TCGA-02-0048-01A-01 1 0.0880 0.90953 0.968 0.000 0.032 0.000 0.000
#> TCGA-02-0060-01A-01 4 0.1697 0.78123 0.060 0.000 0.008 0.932 0.000
#> TCGA-02-0069-01A-01 1 0.1121 0.90936 0.956 0.000 0.044 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.1121 0.90936 0.956 0.000 0.044 0.000 0.000
#> TCGA-02-0080-01A-01 3 0.2935 0.75695 0.120 0.000 0.860 0.004 0.016
#> TCGA-02-0084-01A-03 3 0.4937 0.35890 0.004 0.028 0.604 0.000 0.364
#> TCGA-02-0087-01A-01 3 0.3732 0.73207 0.120 0.000 0.820 0.004 0.056
#> TCGA-02-0104-01A-01 5 0.2243 0.73232 0.056 0.000 0.012 0.016 0.916
#> TCGA-02-0114-01A-01 1 0.0703 0.91068 0.976 0.000 0.024 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.1121 0.90994 0.956 0.000 0.044 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.1357 0.77395 0.004 0.000 0.048 0.000 0.948
#> TCGA-02-0325-01A-01 3 0.2629 0.77064 0.136 0.000 0.860 0.004 0.000
#> TCGA-02-0338-01A-01 1 0.0794 0.91092 0.972 0.000 0.028 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.1430 0.90671 0.944 0.000 0.052 0.004 0.000
#> TCGA-02-0432-01A-02 4 0.7087 0.01816 0.388 0.000 0.192 0.396 0.024
#> TCGA-02-0439-01A-01 3 0.2278 0.76858 0.008 0.000 0.916 0.044 0.032
#> TCGA-02-0440-01A-01 1 0.0566 0.90912 0.984 0.000 0.012 0.000 0.004
#> TCGA-02-0446-01A-01 4 0.2629 0.72483 0.136 0.000 0.004 0.860 0.000
#> TCGA-06-0128-01A-01 4 0.5772 0.52446 0.264 0.072 0.028 0.636 0.000
#> TCGA-06-0129-01A-01 1 0.2230 0.86134 0.884 0.000 0.116 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.4223 0.66805 0.724 0.000 0.248 0.028 0.000
#> TCGA-06-0156-01A-01 1 0.5738 0.59697 0.688 0.208 0.016 0.036 0.052
#> TCGA-06-0166-01A-01 1 0.2961 0.82411 0.872 0.008 0.016 0.004 0.100
#> TCGA-06-0174-01A-01 1 0.1074 0.89748 0.968 0.000 0.016 0.004 0.012
#> TCGA-06-0177-01A-01 1 0.2775 0.84820 0.884 0.000 0.036 0.004 0.076
#> TCGA-06-0238-01A-02 5 0.0771 0.76972 0.000 0.000 0.020 0.004 0.976
#> TCGA-06-0241-01A-02 1 0.1278 0.89308 0.960 0.000 0.020 0.004 0.016
#> TCGA-06-0410-01A-01 1 0.3237 0.81355 0.860 0.000 0.016 0.028 0.096
#> TCGA-06-0413-01A-01 1 0.0963 0.91038 0.964 0.000 0.036 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.1569 0.88690 0.944 0.000 0.008 0.044 0.004
#> TCGA-06-0646-01A-01 1 0.7181 0.47938 0.568 0.124 0.164 0.000 0.144
#> TCGA-06-0648-01A-01 5 0.2889 0.73365 0.084 0.000 0.044 0.000 0.872
#> TCGA-08-0245-01A-01 1 0.1549 0.88196 0.944 0.000 0.016 0.000 0.040
#> TCGA-08-0344-01A-01 1 0.1549 0.88685 0.944 0.000 0.000 0.016 0.040
#> TCGA-08-0347-01A-01 4 0.1597 0.80046 0.008 0.000 0.020 0.948 0.024
#> TCGA-08-0348-01A-01 1 0.0865 0.91032 0.972 0.000 0.024 0.000 0.004
#> TCGA-08-0350-01A-01 5 0.2491 0.76677 0.036 0.000 0.068 0.000 0.896
#> TCGA-08-0353-01A-01 1 0.1478 0.89958 0.936 0.000 0.064 0.000 0.000
#> TCGA-08-0359-01A-01 4 0.0613 0.80744 0.004 0.000 0.004 0.984 0.008
#> TCGA-08-0385-01A-01 5 0.1251 0.77205 0.008 0.000 0.036 0.000 0.956
#> TCGA-08-0517-01A-01 1 0.0865 0.90813 0.972 0.000 0.024 0.000 0.004
#> TCGA-08-0524-01A-01 1 0.1281 0.89790 0.956 0.000 0.012 0.000 0.032
#> TCGA-12-0616-01A-01 5 0.2052 0.72791 0.080 0.000 0.004 0.004 0.912
#> TCGA-12-0618-01A-01 1 0.0833 0.90822 0.976 0.000 0.016 0.004 0.004
#> TCGA-02-0089-01A-01 4 0.1443 0.79785 0.004 0.004 0.044 0.948 0.000
#> TCGA-02-0113-01A-01 3 0.7723 0.10323 0.020 0.368 0.372 0.212 0.028
#> TCGA-02-0115-01A-01 4 0.0404 0.80696 0.000 0.000 0.012 0.988 0.000
#> TCGA-02-0451-01A-01 4 0.1124 0.80158 0.004 0.000 0.036 0.960 0.000
#> TCGA-06-0132-01A-02 4 0.0324 0.80779 0.000 0.000 0.004 0.992 0.004
#> TCGA-06-0133-01A-02 4 0.0451 0.80729 0.004 0.000 0.008 0.988 0.000
#> TCGA-06-0138-01A-02 5 0.5260 0.06821 0.016 0.004 0.016 0.408 0.556
#> TCGA-06-0160-01A-01 4 0.0486 0.80781 0.004 0.000 0.004 0.988 0.004
#> TCGA-06-0162-01A-01 4 0.4854 0.50220 0.008 0.004 0.016 0.636 0.336
#> TCGA-06-0167-01A-01 4 0.0486 0.80781 0.004 0.000 0.004 0.988 0.004
#> TCGA-06-0171-01A-02 4 0.4440 0.66746 0.028 0.000 0.020 0.752 0.200
#> TCGA-06-0173-01A-01 4 0.6523 0.59746 0.064 0.188 0.044 0.656 0.048
#> TCGA-06-0179-01A-02 4 0.0486 0.80835 0.004 0.000 0.004 0.988 0.004
#> TCGA-06-0182-01A-01 5 0.5021 0.59723 0.056 0.012 0.024 0.156 0.752
#> TCGA-06-0185-01A-01 4 0.3386 0.76498 0.012 0.000 0.064 0.856 0.068
#> TCGA-06-0195-01B-01 4 0.0486 0.80835 0.004 0.000 0.004 0.988 0.004
#> TCGA-06-0208-01B-01 4 0.3160 0.77321 0.032 0.000 0.040 0.876 0.052
#> TCGA-06-0214-01A-02 4 0.6805 0.23769 0.036 0.392 0.024 0.488 0.060
#> TCGA-06-0219-01A-01 4 0.5585 0.22102 0.024 0.008 0.016 0.508 0.444
#> TCGA-06-0221-01A-01 4 0.4791 0.48105 0.016 0.000 0.008 0.616 0.360
#> TCGA-06-0237-01A-02 4 0.5630 0.26131 0.016 0.000 0.044 0.528 0.412
#> TCGA-06-0240-01A-02 4 0.0486 0.80835 0.004 0.000 0.004 0.988 0.004
#> TCGA-08-0349-01A-01 4 0.5399 0.10635 0.000 0.000 0.056 0.496 0.448
#> TCGA-08-0380-01A-01 4 0.2086 0.78967 0.000 0.008 0.020 0.924 0.048
#> TCGA-08-0386-01A-01 3 0.6667 0.25978 0.320 0.000 0.432 0.248 0.000
#> TCGA-08-0520-01A-01 5 0.4475 0.65354 0.008 0.000 0.068 0.160 0.764
#> TCGA-02-0007-01A-01 3 0.2471 0.76890 0.136 0.000 0.864 0.000 0.000
#> TCGA-02-0009-01A-01 3 0.1908 0.78472 0.092 0.000 0.908 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.1267 0.78290 0.024 0.000 0.960 0.004 0.012
#> TCGA-02-0021-01A-01 3 0.2074 0.78239 0.104 0.000 0.896 0.000 0.000
#> TCGA-02-0023-01B-01 5 0.2629 0.74609 0.000 0.000 0.136 0.004 0.860
#> TCGA-02-0027-01A-01 3 0.3210 0.70037 0.212 0.000 0.788 0.000 0.000
#> TCGA-02-0038-01A-01 3 0.4565 0.65327 0.016 0.240 0.720 0.024 0.000
#> TCGA-02-0043-01A-01 1 0.4283 0.14472 0.544 0.000 0.456 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.4419 0.39044 0.008 0.004 0.644 0.000 0.344
#> TCGA-02-0102-01A-01 3 0.2020 0.78336 0.100 0.000 0.900 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.2450 0.77307 0.052 0.000 0.900 0.000 0.048
#> TCGA-02-0269-01B-01 3 0.3480 0.60772 0.000 0.000 0.752 0.000 0.248
#> TCGA-02-0285-01A-01 5 0.4276 0.37263 0.000 0.004 0.380 0.000 0.616
#> TCGA-02-0289-01A-01 3 0.1484 0.77083 0.008 0.000 0.944 0.000 0.048
#> TCGA-02-0290-01A-01 5 0.1478 0.77232 0.000 0.000 0.064 0.000 0.936
#> TCGA-02-0317-01A-01 5 0.2424 0.74950 0.000 0.000 0.132 0.000 0.868
#> TCGA-02-0333-01A-02 3 0.2719 0.71901 0.004 0.000 0.852 0.000 0.144
#> TCGA-02-0422-01A-01 5 0.4675 0.20878 0.008 0.004 0.444 0.000 0.544
#> TCGA-02-0430-01A-01 3 0.2891 0.74467 0.176 0.000 0.824 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.1965 0.78417 0.096 0.000 0.904 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.1965 0.78456 0.096 0.000 0.904 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.2344 0.78367 0.032 0.000 0.904 0.064 0.000
#> TCGA-06-0145-01A-04 3 0.2291 0.78727 0.036 0.056 0.908 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.1690 0.78253 0.024 0.008 0.944 0.000 0.024
#> TCGA-06-0187-01A-01 3 0.3051 0.76212 0.028 0.120 0.852 0.000 0.000
#> TCGA-06-0211-01B-01 5 0.7273 0.37679 0.224 0.000 0.224 0.052 0.500
#> TCGA-06-0402-01A-01 1 0.2719 0.82388 0.852 0.000 0.144 0.004 0.000
#> TCGA-08-0246-01A-01 3 0.5901 0.00725 0.004 0.064 0.476 0.008 0.448
#> TCGA-08-0354-01A-01 5 0.0727 0.76574 0.000 0.004 0.012 0.004 0.980
#> TCGA-08-0355-01A-01 3 0.4287 0.08738 0.000 0.000 0.540 0.000 0.460
#> TCGA-08-0357-01A-01 3 0.4610 0.14140 0.012 0.000 0.556 0.000 0.432
#> TCGA-08-0358-01A-01 5 0.1478 0.77232 0.000 0.000 0.064 0.000 0.936
#> TCGA-08-0375-01A-01 3 0.4254 0.61997 0.040 0.000 0.740 0.000 0.220
#> TCGA-08-0511-01A-01 3 0.3175 0.78585 0.044 0.020 0.872 0.064 0.000
#> TCGA-08-0514-01A-01 3 0.2484 0.78398 0.028 0.068 0.900 0.000 0.004
#> TCGA-08-0518-01A-01 3 0.1965 0.78417 0.096 0.000 0.904 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.1757 0.79133 0.048 0.012 0.936 0.000 0.004
#> TCGA-08-0531-01A-01 3 0.1648 0.78733 0.040 0.000 0.940 0.000 0.020
#> TCGA-02-0057-01A-01 3 0.2966 0.75458 0.000 0.136 0.848 0.016 0.000
#> TCGA-02-0004-01A-01 2 0.1430 0.92477 0.000 0.944 0.004 0.000 0.052
#> TCGA-02-0006-01B-01 2 0.0162 0.94246 0.000 0.996 0.004 0.000 0.000
#> TCGA-02-0025-01A-01 5 0.5234 0.23095 0.000 0.460 0.044 0.000 0.496
#> TCGA-02-0033-01A-01 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.2712 0.84315 0.000 0.880 0.032 0.000 0.088
#> TCGA-02-0051-01A-01 2 0.4566 0.59815 0.016 0.700 0.016 0.000 0.268
#> TCGA-02-0054-01A-01 2 0.0693 0.93909 0.000 0.980 0.012 0.008 0.000
#> TCGA-02-0055-01A-01 2 0.2037 0.90918 0.012 0.920 0.004 0.000 0.064
#> TCGA-02-0059-01A-01 5 0.4749 0.43700 0.016 0.348 0.008 0.000 0.628
#> TCGA-02-0064-01A-01 2 0.0794 0.92973 0.000 0.972 0.028 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.0963 0.92416 0.000 0.964 0.036 0.000 0.000
#> TCGA-02-0079-01A-03 5 0.2236 0.77243 0.000 0.024 0.068 0.000 0.908
#> TCGA-02-0085-01A-01 4 0.0671 0.80506 0.000 0.016 0.004 0.980 0.000
#> TCGA-02-0086-01A-01 2 0.2141 0.91789 0.008 0.928 0.036 0.008 0.020
#> TCGA-02-0099-01A-01 2 0.0290 0.94176 0.000 0.992 0.008 0.000 0.000
#> TCGA-02-0106-01A-01 2 0.2672 0.89698 0.020 0.900 0.016 0.004 0.060
#> TCGA-02-0107-01A-01 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.1341 0.92158 0.000 0.944 0.000 0.000 0.056
#> TCGA-02-0326-01A-01 5 0.1704 0.77162 0.004 0.000 0.068 0.000 0.928
#> TCGA-02-0337-01A-01 5 0.5622 0.34375 0.000 0.416 0.076 0.000 0.508
#> TCGA-06-0122-01A-01 3 0.2674 0.75626 0.004 0.140 0.856 0.000 0.000
#> TCGA-06-0124-01A-01 2 0.3039 0.72160 0.000 0.808 0.192 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.3774 0.62299 0.000 0.296 0.704 0.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.3492 0.71243 0.000 0.188 0.796 0.000 0.016
#> TCGA-06-0152-01A-02 5 0.1544 0.77174 0.000 0.000 0.068 0.000 0.932
#> TCGA-06-0154-01A-02 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.2981 0.89277 0.024 0.892 0.024 0.048 0.012
#> TCGA-06-0176-01A-03 2 0.1857 0.91525 0.008 0.928 0.004 0.000 0.060
#> TCGA-06-0184-01A-01 2 0.2731 0.84938 0.004 0.876 0.016 0.104 0.000
#> TCGA-06-0189-01A-05 2 0.3935 0.72015 0.008 0.760 0.012 0.000 0.220
#> TCGA-06-0190-01A-01 2 0.0290 0.94304 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0194-01A-01 2 0.0703 0.93895 0.000 0.976 0.000 0.000 0.024
#> TCGA-06-0197-01A-02 2 0.2359 0.90520 0.004 0.912 0.016 0.008 0.060
#> TCGA-06-0210-01A-01 2 0.1652 0.92716 0.004 0.944 0.008 0.004 0.040
#> TCGA-06-0397-01A-01 2 0.0898 0.93928 0.008 0.972 0.000 0.000 0.020
#> TCGA-06-0409-01A-02 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.1430 0.91119 0.000 0.944 0.052 0.004 0.000
#> TCGA-06-0644-01A-02 2 0.1502 0.92229 0.000 0.940 0.004 0.000 0.056
#> TCGA-06-0645-01A-01 2 0.0290 0.94190 0.000 0.992 0.000 0.000 0.008
#> TCGA-08-0346-01A-01 5 0.5039 0.28491 0.000 0.456 0.032 0.000 0.512
#> TCGA-08-0352-01A-01 3 0.5575 0.61267 0.000 0.148 0.640 0.212 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0390-01A-01 5 0.3807 0.65818 0.000 0.204 0.012 0.008 0.776
#> TCGA-08-0392-01A-01 5 0.1857 0.74683 0.008 0.060 0.004 0.000 0.928
#> TCGA-08-0509-01A-01 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.3561 0.65309 0.000 0.260 0.740 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.94362 0.000 1.000 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0566 0.94160 0.004 0.984 0.000 0.000 0.012
#> TCGA-12-0620-01A-01 5 0.1740 0.77622 0.000 0.012 0.056 0.000 0.932
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.1970 0.8904 0.912 0.000 0.000 0.028 0.000 0.060
#> TCGA-02-0010-01A-01 1 0.0260 0.9166 0.992 0.000 0.000 0.008 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.1268 0.9031 0.952 0.000 0.004 0.036 0.008 0.000
#> TCGA-02-0014-01A-01 1 0.0632 0.9176 0.976 0.000 0.000 0.024 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0865 0.9075 0.964 0.000 0.000 0.000 0.000 0.036
#> TCGA-02-0026-01B-01 1 0.0912 0.9099 0.972 0.000 0.008 0.012 0.004 0.004
#> TCGA-02-0028-01A-01 1 0.0713 0.9174 0.972 0.000 0.000 0.028 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0713 0.9179 0.972 0.000 0.000 0.028 0.000 0.000
#> TCGA-02-0047-01A-01 6 0.0865 0.7984 0.000 0.000 0.000 0.036 0.000 0.964
#> TCGA-02-0048-01A-01 1 0.2362 0.8638 0.860 0.000 0.004 0.136 0.000 0.000
#> TCGA-02-0060-01A-01 6 0.1946 0.7388 0.072 0.000 0.000 0.012 0.004 0.912
#> TCGA-02-0069-01A-01 1 0.0260 0.9166 0.992 0.000 0.000 0.008 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0363 0.9180 0.988 0.000 0.000 0.012 0.000 0.000
#> TCGA-02-0080-01A-01 3 0.6464 0.5389 0.144 0.000 0.612 0.048 0.144 0.052
#> TCGA-02-0084-01A-03 5 0.6922 0.1066 0.060 0.004 0.324 0.048 0.492 0.072
#> TCGA-02-0087-01A-01 3 0.7428 0.3368 0.108 0.000 0.468 0.048 0.272 0.104
#> TCGA-02-0104-01A-01 5 0.3320 0.6256 0.016 0.000 0.000 0.212 0.772 0.000
#> TCGA-02-0114-01A-01 1 0.1387 0.9059 0.932 0.000 0.000 0.068 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0146 0.9165 0.996 0.000 0.000 0.004 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.0291 0.7494 0.004 0.000 0.000 0.004 0.992 0.000
#> TCGA-02-0325-01A-01 3 0.5441 0.5833 0.188 0.000 0.680 0.044 0.020 0.068
#> TCGA-02-0338-01A-01 1 0.0146 0.9173 0.996 0.000 0.000 0.004 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.1894 0.8896 0.928 0.000 0.012 0.016 0.004 0.040
#> TCGA-02-0432-01A-02 6 0.7497 0.1823 0.328 0.000 0.060 0.048 0.164 0.400
#> TCGA-02-0439-01A-01 3 0.5480 0.5920 0.000 0.000 0.656 0.044 0.164 0.136
#> TCGA-02-0440-01A-01 1 0.0937 0.9145 0.960 0.000 0.000 0.040 0.000 0.000
#> TCGA-02-0446-01A-01 6 0.2378 0.6815 0.152 0.000 0.000 0.000 0.000 0.848
#> TCGA-06-0128-01A-01 4 0.6168 0.2078 0.324 0.000 0.012 0.476 0.004 0.184
#> TCGA-06-0129-01A-01 1 0.1723 0.8873 0.928 0.000 0.036 0.036 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.5443 0.6045 0.680 0.000 0.160 0.048 0.008 0.104
#> TCGA-06-0156-01A-01 1 0.4410 0.3342 0.560 0.028 0.000 0.412 0.000 0.000
#> TCGA-06-0166-01A-01 1 0.3109 0.7452 0.772 0.004 0.000 0.224 0.000 0.000
#> TCGA-06-0174-01A-01 1 0.1610 0.8987 0.916 0.000 0.000 0.084 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.2402 0.8618 0.896 0.000 0.000 0.012 0.060 0.032
#> TCGA-06-0238-01A-02 5 0.0458 0.7492 0.000 0.000 0.000 0.016 0.984 0.000
#> TCGA-06-0241-01A-02 1 0.1765 0.8938 0.904 0.000 0.000 0.096 0.000 0.000
#> TCGA-06-0410-01A-01 4 0.3330 0.4423 0.284 0.000 0.000 0.716 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.9167 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.1204 0.9094 0.944 0.000 0.000 0.056 0.000 0.000
#> TCGA-06-0646-01A-01 1 0.4699 0.6684 0.732 0.120 0.020 0.004 0.124 0.000
#> TCGA-06-0648-01A-01 5 0.1901 0.7207 0.076 0.000 0.000 0.004 0.912 0.008
#> TCGA-08-0245-01A-01 1 0.1663 0.8984 0.912 0.000 0.000 0.088 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.1036 0.9121 0.964 0.000 0.000 0.008 0.004 0.024
#> TCGA-08-0347-01A-01 6 0.2312 0.7165 0.012 0.000 0.000 0.000 0.112 0.876
#> TCGA-08-0348-01A-01 1 0.0000 0.9167 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-08-0350-01A-01 5 0.2745 0.6840 0.112 0.000 0.000 0.020 0.860 0.008
#> TCGA-08-0353-01A-01 1 0.3172 0.8139 0.832 0.000 0.092 0.076 0.000 0.000
#> TCGA-08-0359-01A-01 6 0.0000 0.7934 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-08-0385-01A-01 5 0.0717 0.7500 0.008 0.000 0.000 0.016 0.976 0.000
#> TCGA-08-0517-01A-01 1 0.1501 0.9022 0.924 0.000 0.000 0.076 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0713 0.9173 0.972 0.000 0.000 0.028 0.000 0.000
#> TCGA-12-0616-01A-01 5 0.3732 0.6381 0.076 0.000 0.000 0.144 0.780 0.000
#> TCGA-12-0618-01A-01 1 0.0146 0.9167 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-02-0089-01A-01 6 0.4878 0.2069 0.000 0.000 0.060 0.424 0.000 0.516
#> TCGA-02-0113-01A-01 4 0.3302 0.5731 0.000 0.004 0.232 0.760 0.000 0.004
#> TCGA-02-0115-01A-01 6 0.2948 0.6990 0.000 0.000 0.008 0.188 0.000 0.804
#> TCGA-02-0451-01A-01 6 0.4576 0.3090 0.000 0.000 0.040 0.400 0.000 0.560
#> TCGA-06-0132-01A-02 6 0.0713 0.7987 0.000 0.000 0.000 0.028 0.000 0.972
#> TCGA-06-0133-01A-02 6 0.3672 0.5461 0.000 0.000 0.008 0.304 0.000 0.688
#> TCGA-06-0138-01A-02 4 0.5353 0.3037 0.000 0.000 0.000 0.528 0.352 0.120
#> TCGA-06-0160-01A-01 6 0.0146 0.7951 0.000 0.000 0.000 0.004 0.000 0.996
#> TCGA-06-0162-01A-01 4 0.5714 0.3525 0.000 0.000 0.000 0.508 0.296 0.196
#> TCGA-06-0167-01A-01 6 0.0260 0.7963 0.000 0.000 0.000 0.008 0.000 0.992
#> TCGA-06-0171-01A-02 4 0.3284 0.5769 0.000 0.000 0.000 0.800 0.032 0.168
#> TCGA-06-0173-01A-01 4 0.2420 0.6340 0.000 0.004 0.032 0.888 0.000 0.076
#> TCGA-06-0179-01A-02 6 0.1267 0.7925 0.000 0.000 0.000 0.060 0.000 0.940
#> TCGA-06-0182-01A-01 4 0.1714 0.6353 0.000 0.000 0.000 0.908 0.092 0.000
#> TCGA-06-0185-01A-01 4 0.3618 0.6224 0.000 0.000 0.104 0.808 0.008 0.080
#> TCGA-06-0195-01B-01 6 0.1327 0.7910 0.000 0.000 0.000 0.064 0.000 0.936
#> TCGA-06-0208-01B-01 4 0.2346 0.6128 0.000 0.000 0.008 0.868 0.000 0.124
#> TCGA-06-0214-01A-02 4 0.2716 0.6111 0.000 0.008 0.004 0.852 0.004 0.132
#> TCGA-06-0219-01A-01 4 0.4887 0.4163 0.000 0.000 0.000 0.612 0.300 0.088
#> TCGA-06-0221-01A-01 5 0.5862 0.0375 0.000 0.000 0.000 0.344 0.452 0.204
#> TCGA-06-0237-01A-02 4 0.2982 0.6382 0.000 0.000 0.012 0.860 0.060 0.068
#> TCGA-06-0240-01A-02 6 0.1141 0.7951 0.000 0.000 0.000 0.052 0.000 0.948
#> TCGA-08-0349-01A-01 5 0.4692 0.4325 0.000 0.000 0.000 0.080 0.644 0.276
#> TCGA-08-0380-01A-01 6 0.3979 0.6217 0.000 0.000 0.004 0.244 0.032 0.720
#> TCGA-08-0386-01A-01 4 0.5891 0.3004 0.076 0.000 0.348 0.524 0.000 0.052
#> TCGA-08-0520-01A-01 4 0.4218 0.2800 0.000 0.000 0.012 0.584 0.400 0.004
#> TCGA-02-0007-01A-01 3 0.2877 0.6765 0.012 0.000 0.820 0.168 0.000 0.000
#> TCGA-02-0009-01A-01 3 0.0790 0.7417 0.000 0.000 0.968 0.032 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.2152 0.7367 0.000 0.000 0.904 0.024 0.068 0.004
#> TCGA-02-0021-01A-01 3 0.1958 0.7192 0.004 0.000 0.896 0.100 0.000 0.000
#> TCGA-02-0023-01B-01 5 0.1155 0.7413 0.000 0.000 0.036 0.004 0.956 0.004
#> TCGA-02-0027-01A-01 3 0.5082 0.5028 0.284 0.000 0.640 0.040 0.008 0.028
#> TCGA-02-0038-01A-01 4 0.3737 0.2955 0.000 0.000 0.392 0.608 0.000 0.000
#> TCGA-02-0043-01A-01 3 0.3634 0.5046 0.296 0.000 0.696 0.008 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.4279 0.2840 0.004 0.000 0.548 0.012 0.436 0.000
#> TCGA-02-0102-01A-01 3 0.1124 0.7423 0.008 0.000 0.956 0.036 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.3890 0.6751 0.036 0.000 0.784 0.028 0.152 0.000
#> TCGA-02-0269-01B-01 3 0.4147 0.3240 0.000 0.000 0.552 0.012 0.436 0.000
#> TCGA-02-0285-01A-01 5 0.4095 -0.0797 0.000 0.000 0.480 0.008 0.512 0.000
#> TCGA-02-0289-01A-01 3 0.1757 0.7404 0.000 0.000 0.916 0.008 0.076 0.000
#> TCGA-02-0290-01A-01 5 0.1327 0.7340 0.000 0.000 0.000 0.064 0.936 0.000
#> TCGA-02-0317-01A-01 5 0.1588 0.7228 0.000 0.000 0.072 0.004 0.924 0.000
#> TCGA-02-0333-01A-02 3 0.3974 0.5601 0.000 0.000 0.680 0.024 0.296 0.000
#> TCGA-02-0422-01A-01 3 0.5571 0.2453 0.000 0.000 0.496 0.148 0.356 0.000
#> TCGA-02-0430-01A-01 3 0.3088 0.6599 0.020 0.000 0.808 0.172 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0806 0.7427 0.008 0.000 0.972 0.020 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.0405 0.7425 0.004 0.000 0.988 0.008 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.0777 0.7425 0.000 0.000 0.972 0.024 0.000 0.004
#> TCGA-06-0145-01A-04 3 0.1267 0.7353 0.000 0.000 0.940 0.060 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.1124 0.7437 0.000 0.000 0.956 0.008 0.036 0.000
#> TCGA-06-0187-01A-01 3 0.3857 0.0701 0.000 0.000 0.532 0.468 0.000 0.000
#> TCGA-06-0211-01B-01 4 0.2742 0.6343 0.000 0.000 0.128 0.852 0.012 0.008
#> TCGA-06-0402-01A-01 4 0.6089 0.1585 0.308 0.000 0.300 0.392 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.5801 0.3150 0.000 0.000 0.492 0.216 0.292 0.000
#> TCGA-08-0354-01A-01 5 0.2527 0.6628 0.000 0.000 0.000 0.168 0.832 0.000
#> TCGA-08-0355-01A-01 5 0.3695 0.1875 0.000 0.000 0.376 0.000 0.624 0.000
#> TCGA-08-0357-01A-01 3 0.4648 0.3147 0.000 0.000 0.548 0.044 0.408 0.000
#> TCGA-08-0358-01A-01 5 0.0260 0.7489 0.000 0.000 0.000 0.008 0.992 0.000
#> TCGA-08-0375-01A-01 3 0.3512 0.5969 0.000 0.000 0.720 0.008 0.272 0.000
#> TCGA-08-0511-01A-01 3 0.1713 0.7394 0.000 0.000 0.928 0.044 0.000 0.028
#> TCGA-08-0514-01A-01 3 0.2632 0.6727 0.000 0.000 0.832 0.164 0.004 0.000
#> TCGA-08-0518-01A-01 3 0.1219 0.7390 0.004 0.000 0.948 0.048 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.2146 0.7098 0.000 0.000 0.880 0.116 0.004 0.000
#> TCGA-08-0531-01A-01 3 0.3314 0.6013 0.000 0.000 0.764 0.224 0.012 0.000
#> TCGA-02-0057-01A-01 3 0.2415 0.7321 0.000 0.032 0.904 0.036 0.004 0.024
#> TCGA-02-0004-01A-01 2 0.0865 0.8639 0.000 0.964 0.000 0.036 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.1007 0.8595 0.000 0.956 0.000 0.044 0.000 0.000
#> TCGA-02-0025-01A-01 2 0.2941 0.6829 0.000 0.780 0.000 0.000 0.220 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.1908 0.8219 0.000 0.900 0.000 0.004 0.096 0.000
#> TCGA-02-0051-01A-01 2 0.5133 0.5048 0.000 0.624 0.000 0.164 0.212 0.000
#> TCGA-02-0054-01A-01 2 0.3541 0.6798 0.000 0.748 0.020 0.232 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.0547 0.8701 0.000 0.980 0.000 0.020 0.000 0.000
#> TCGA-02-0059-01A-01 5 0.4570 0.5703 0.000 0.152 0.000 0.148 0.700 0.000
#> TCGA-02-0064-01A-01 2 0.0405 0.8699 0.000 0.988 0.008 0.004 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.1643 0.8388 0.000 0.924 0.068 0.008 0.000 0.000
#> TCGA-02-0079-01A-03 5 0.1757 0.7357 0.000 0.052 0.000 0.008 0.928 0.012
#> TCGA-02-0085-01A-01 6 0.0363 0.7923 0.000 0.012 0.000 0.000 0.000 0.988
#> TCGA-02-0086-01A-01 4 0.3599 0.5260 0.000 0.220 0.020 0.756 0.004 0.000
#> TCGA-02-0099-01A-01 2 0.2473 0.7838 0.000 0.856 0.008 0.136 0.000 0.000
#> TCGA-02-0106-01A-01 2 0.4276 0.4018 0.000 0.564 0.000 0.416 0.020 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0972 0.8638 0.000 0.964 0.000 0.008 0.028 0.000
#> TCGA-02-0326-01A-01 5 0.1176 0.7422 0.000 0.000 0.000 0.020 0.956 0.024
#> TCGA-02-0337-01A-01 2 0.4490 0.3669 0.000 0.596 0.000 0.024 0.372 0.008
#> TCGA-06-0122-01A-01 3 0.1219 0.7366 0.000 0.048 0.948 0.004 0.000 0.000
#> TCGA-06-0124-01A-01 2 0.2703 0.7467 0.000 0.824 0.172 0.004 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0143-01A-01 2 0.4093 0.5444 0.000 0.680 0.292 0.024 0.000 0.004
#> TCGA-06-0147-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.2945 0.7342 0.000 0.048 0.864 0.016 0.072 0.000
#> TCGA-06-0152-01A-02 5 0.0000 0.7488 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0154-01A-02 2 0.0260 0.8722 0.000 0.992 0.000 0.008 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.6750 0.2783 0.036 0.496 0.084 0.324 0.000 0.060
#> TCGA-06-0176-01A-03 2 0.0363 0.8716 0.000 0.988 0.000 0.012 0.000 0.000
#> TCGA-06-0184-01A-01 4 0.4798 0.5783 0.000 0.144 0.040 0.740 0.012 0.064
#> TCGA-06-0189-01A-05 5 0.6024 0.1479 0.000 0.328 0.000 0.256 0.416 0.000
#> TCGA-06-0190-01A-01 2 0.0146 0.8726 0.000 0.996 0.000 0.004 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.1501 0.8430 0.000 0.924 0.000 0.076 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.3464 0.5960 0.000 0.688 0.000 0.312 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.4379 0.5049 0.000 0.632 0.008 0.336 0.024 0.000
#> TCGA-06-0397-01A-01 2 0.1196 0.8623 0.000 0.952 0.008 0.040 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.5786 0.2163 0.000 0.504 0.240 0.256 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.1501 0.8423 0.000 0.924 0.000 0.076 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0346-01A-01 5 0.3966 0.1548 0.000 0.444 0.000 0.004 0.552 0.000
#> TCGA-08-0352-01A-01 3 0.6785 0.3958 0.000 0.124 0.504 0.012 0.080 0.280
#> TCGA-08-0360-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0390-01A-01 5 0.3595 0.6689 0.000 0.084 0.000 0.120 0.796 0.000
#> TCGA-08-0392-01A-01 5 0.2692 0.6772 0.000 0.012 0.000 0.148 0.840 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.1858 0.7224 0.000 0.004 0.904 0.092 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.8733 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0620-01A-01 5 0.0291 0.7496 0.000 0.004 0.000 0.004 0.992 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> CV:NMF 159 1.46e-11 2
#> CV:NMF 147 8.46e-28 3
#> CV:NMF 150 3.61e-34 4
#> CV:NMF 150 6.42e-50 5
#> CV:NMF 141 1.77e-47 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "hclust"]
# you can also extract it by
# res = res_list["MAD:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.280 0.649 0.825 0.4418 0.525 0.525
#> 3 3 0.275 0.501 0.734 0.3707 0.836 0.688
#> 4 4 0.416 0.588 0.759 0.1698 0.798 0.504
#> 5 5 0.485 0.494 0.722 0.0639 0.935 0.761
#> 6 6 0.531 0.476 0.698 0.0362 0.966 0.856
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.3733 0.7685 0.928 0.072
#> TCGA-02-0010-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0938 0.7525 0.988 0.012
#> TCGA-02-0014-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.2043 0.7601 0.968 0.032
#> TCGA-02-0028-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.3733 0.7685 0.928 0.072
#> TCGA-02-0047-01A-01 1 0.8016 0.7143 0.756 0.244
#> TCGA-02-0048-01A-01 1 0.4022 0.7638 0.920 0.080
#> TCGA-02-0060-01A-01 1 0.5294 0.7662 0.880 0.120
#> TCGA-02-0069-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.3733 0.7677 0.928 0.072
#> TCGA-02-0080-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0084-01A-03 1 0.5519 0.7520 0.872 0.128
#> TCGA-02-0087-01A-01 1 0.5519 0.7520 0.872 0.128
#> TCGA-02-0104-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.6887 0.7512 0.816 0.184
#> TCGA-02-0325-01A-01 1 0.6887 0.7512 0.816 0.184
#> TCGA-02-0338-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.7474 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.4298 0.7636 0.912 0.088
#> TCGA-02-0440-01A-01 1 0.3733 0.7677 0.928 0.072
#> TCGA-02-0446-01A-01 1 0.7950 0.7150 0.760 0.240
#> TCGA-06-0128-01A-01 1 0.0672 0.7512 0.992 0.008
#> TCGA-06-0129-01A-01 1 0.0672 0.7512 0.992 0.008
#> TCGA-06-0146-01A-01 1 0.1414 0.7547 0.980 0.020
#> TCGA-06-0156-01A-01 1 0.8267 0.6979 0.740 0.260
#> TCGA-06-0166-01A-01 1 0.6801 0.7534 0.820 0.180
#> TCGA-06-0174-01A-01 1 0.3733 0.7685 0.928 0.072
#> TCGA-06-0177-01A-01 1 0.3879 0.7680 0.924 0.076
#> TCGA-06-0238-01A-02 1 0.3584 0.7680 0.932 0.068
#> TCGA-06-0241-01A-02 1 0.1843 0.7575 0.972 0.028
#> TCGA-06-0410-01A-01 1 0.1843 0.7575 0.972 0.028
#> TCGA-06-0413-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.3114 0.7660 0.944 0.056
#> TCGA-06-0646-01A-01 1 0.8267 0.6979 0.740 0.260
#> TCGA-06-0648-01A-01 1 0.2043 0.7601 0.968 0.032
#> TCGA-08-0245-01A-01 1 0.1843 0.7575 0.972 0.028
#> TCGA-08-0344-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.7950 0.7150 0.760 0.240
#> TCGA-08-0348-01A-01 1 0.4690 0.7674 0.900 0.100
#> TCGA-08-0350-01A-01 1 0.1414 0.7547 0.980 0.020
#> TCGA-08-0353-01A-01 1 0.7376 0.7311 0.792 0.208
#> TCGA-08-0359-01A-01 1 0.7453 0.7317 0.788 0.212
#> TCGA-08-0385-01A-01 1 0.0938 0.7525 0.988 0.012
#> TCGA-08-0517-01A-01 1 0.2423 0.7602 0.960 0.040
#> TCGA-08-0524-01A-01 1 0.0000 0.7474 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.2423 0.7609 0.960 0.040
#> TCGA-12-0618-01A-01 1 0.2043 0.7601 0.968 0.032
#> TCGA-02-0089-01A-01 2 0.9850 0.1650 0.428 0.572
#> TCGA-02-0113-01A-01 1 0.9522 0.5916 0.628 0.372
#> TCGA-02-0115-01A-01 1 0.9460 0.5188 0.636 0.364
#> TCGA-02-0451-01A-01 1 0.9998 0.1559 0.508 0.492
#> TCGA-06-0132-01A-02 1 0.9427 0.5249 0.640 0.360
#> TCGA-06-0133-01A-02 1 0.6438 0.7521 0.836 0.164
#> TCGA-06-0138-01A-02 1 0.8763 0.6575 0.704 0.296
#> TCGA-06-0160-01A-01 1 0.0376 0.7495 0.996 0.004
#> TCGA-06-0162-01A-01 1 0.6712 0.7466 0.824 0.176
#> TCGA-06-0167-01A-01 1 0.0376 0.7495 0.996 0.004
#> TCGA-06-0171-01A-02 1 0.8713 0.6608 0.708 0.292
#> TCGA-06-0173-01A-01 2 0.9661 0.2777 0.392 0.608
#> TCGA-06-0179-01A-02 1 0.9427 0.5249 0.640 0.360
#> TCGA-06-0182-01A-01 1 0.8909 0.6681 0.692 0.308
#> TCGA-06-0185-01A-01 1 0.9393 0.6114 0.644 0.356
#> TCGA-06-0195-01B-01 1 0.5059 0.7626 0.888 0.112
#> TCGA-06-0208-01B-01 1 0.6343 0.7533 0.840 0.160
#> TCGA-06-0214-01A-02 1 0.9993 0.1836 0.516 0.484
#> TCGA-06-0219-01A-01 1 0.5842 0.7586 0.860 0.140
#> TCGA-06-0221-01A-01 1 0.4815 0.7627 0.896 0.104
#> TCGA-06-0237-01A-02 1 0.6712 0.7481 0.824 0.176
#> TCGA-06-0240-01A-02 1 0.0376 0.7495 0.996 0.004
#> TCGA-08-0349-01A-01 1 0.8861 0.6549 0.696 0.304
#> TCGA-08-0380-01A-01 1 0.9580 0.4839 0.620 0.380
#> TCGA-08-0386-01A-01 1 0.9087 0.6531 0.676 0.324
#> TCGA-08-0520-01A-01 1 0.8861 0.6725 0.696 0.304
#> TCGA-02-0007-01A-01 1 0.9129 0.6493 0.672 0.328
#> TCGA-02-0009-01A-01 1 0.9608 0.5687 0.616 0.384
#> TCGA-02-0016-01A-01 1 0.9491 0.5937 0.632 0.368
#> TCGA-02-0021-01A-01 1 0.9608 0.5687 0.616 0.384
#> TCGA-02-0023-01B-01 2 0.9833 0.0553 0.424 0.576
#> TCGA-02-0027-01A-01 1 0.6438 0.7600 0.836 0.164
#> TCGA-02-0038-01A-01 2 0.9580 0.3015 0.380 0.620
#> TCGA-02-0043-01A-01 1 0.9608 0.5687 0.616 0.384
#> TCGA-02-0070-01A-01 2 0.3733 0.7789 0.072 0.928
#> TCGA-02-0102-01A-01 1 0.9661 0.5551 0.608 0.392
#> TCGA-02-0260-01A-03 1 0.9248 0.6296 0.660 0.340
#> TCGA-02-0269-01B-01 1 0.9248 0.6296 0.660 0.340
#> TCGA-02-0285-01A-01 1 0.9850 0.4833 0.572 0.428
#> TCGA-02-0289-01A-01 1 0.9580 0.5744 0.620 0.380
#> TCGA-02-0290-01A-01 1 0.9815 0.4997 0.580 0.420
#> TCGA-02-0317-01A-01 1 0.9209 0.6335 0.664 0.336
#> TCGA-02-0333-01A-02 1 0.9248 0.6296 0.660 0.340
#> TCGA-02-0422-01A-01 1 0.9993 0.3282 0.516 0.484
#> TCGA-02-0430-01A-01 1 0.9850 0.4833 0.572 0.428
#> TCGA-06-0125-01A-01 1 0.9608 0.5687 0.616 0.384
#> TCGA-06-0126-01A-01 1 0.9608 0.5687 0.616 0.384
#> TCGA-06-0137-01A-03 1 0.9522 0.5871 0.628 0.372
#> TCGA-06-0145-01A-04 1 0.9922 0.4340 0.552 0.448
#> TCGA-06-0148-01A-01 1 0.9732 0.5330 0.596 0.404
#> TCGA-06-0187-01A-01 2 0.9996 -0.2437 0.488 0.512
#> TCGA-06-0211-01B-01 1 0.9635 0.5626 0.612 0.388
#> TCGA-06-0402-01A-01 1 0.9608 0.5687 0.616 0.384
#> TCGA-08-0246-01A-01 2 0.9710 0.1568 0.400 0.600
#> TCGA-08-0354-01A-01 2 0.9754 0.1153 0.408 0.592
#> TCGA-08-0355-01A-01 2 0.9635 0.1978 0.388 0.612
#> TCGA-08-0357-01A-01 1 0.9993 0.3282 0.516 0.484
#> TCGA-08-0358-01A-01 1 0.9209 0.6335 0.664 0.336
#> TCGA-08-0375-01A-01 1 0.9286 0.6250 0.656 0.344
#> TCGA-08-0511-01A-01 2 0.9996 -0.2516 0.488 0.512
#> TCGA-08-0514-01A-01 2 0.9983 -0.2048 0.476 0.524
#> TCGA-08-0518-01A-01 1 0.9686 0.5475 0.604 0.396
#> TCGA-08-0529-01A-02 1 0.9850 0.4833 0.572 0.428
#> TCGA-08-0531-01A-01 1 0.9661 0.5549 0.608 0.392
#> TCGA-02-0057-01A-01 2 0.9815 0.1838 0.420 0.580
#> TCGA-02-0004-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.9393 0.3762 0.356 0.644
#> TCGA-02-0025-01A-01 2 0.0938 0.8056 0.012 0.988
#> TCGA-02-0033-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0672 0.8074 0.008 0.992
#> TCGA-02-0039-01A-01 2 0.5178 0.7465 0.116 0.884
#> TCGA-02-0051-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.8555 0.5527 0.280 0.720
#> TCGA-02-0055-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0376 0.8069 0.004 0.996
#> TCGA-02-0075-01A-01 2 0.0938 0.8069 0.012 0.988
#> TCGA-02-0079-01A-03 2 0.8813 0.5225 0.300 0.700
#> TCGA-02-0085-01A-01 2 0.9000 0.5046 0.316 0.684
#> TCGA-02-0086-01A-01 2 0.0938 0.8069 0.012 0.988
#> TCGA-02-0099-01A-01 2 0.7528 0.6512 0.216 0.784
#> TCGA-02-0106-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-02-0326-01A-01 1 0.9286 0.5869 0.656 0.344
#> TCGA-02-0337-01A-01 2 0.8555 0.5609 0.280 0.720
#> TCGA-06-0122-01A-01 2 0.3274 0.7890 0.060 0.940
#> TCGA-06-0124-01A-01 2 0.0938 0.8069 0.012 0.988
#> TCGA-06-0130-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.3274 0.7867 0.060 0.940
#> TCGA-06-0147-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.9170 0.3862 0.332 0.668
#> TCGA-06-0152-01A-02 2 0.9833 0.0494 0.424 0.576
#> TCGA-06-0154-01A-02 2 0.0938 0.8069 0.012 0.988
#> TCGA-06-0164-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.6801 0.6704 0.180 0.820
#> TCGA-06-0176-01A-03 2 0.0000 0.8064 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.9881 0.1085 0.436 0.564
#> TCGA-06-0189-01A-05 2 0.0000 0.8064 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0938 0.8069 0.012 0.988
#> TCGA-06-0194-01A-01 2 0.1633 0.8038 0.024 0.976
#> TCGA-06-0197-01A-02 2 0.0000 0.8064 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.2948 0.7909 0.052 0.948
#> TCGA-06-0397-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.8064 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.2948 0.7909 0.052 0.948
#> TCGA-06-0644-01A-02 2 0.0000 0.8064 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0938 0.8066 0.012 0.988
#> TCGA-08-0346-01A-01 2 0.2423 0.7971 0.040 0.960
#> TCGA-08-0352-01A-01 2 0.5519 0.7426 0.128 0.872
#> TCGA-08-0360-01A-01 2 0.0672 0.8074 0.008 0.992
#> TCGA-08-0390-01A-01 2 0.8955 0.5136 0.312 0.688
#> TCGA-08-0392-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.2423 0.7930 0.040 0.960
#> TCGA-08-0510-01A-01 2 0.1184 0.8059 0.016 0.984
#> TCGA-08-0512-01A-01 2 0.0376 0.8069 0.004 0.996
#> TCGA-08-0522-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.8064 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.8327 0.5291 0.264 0.736
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.5689 0.58121 0.780 0.036 0.184
#> TCGA-02-0010-01A-01 1 0.0000 0.58856 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.5831 0.41081 0.708 0.008 0.284
#> TCGA-02-0014-01A-01 1 0.0000 0.58856 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0237 0.58907 0.996 0.000 0.004
#> TCGA-02-0026-01B-01 1 0.4602 0.56030 0.832 0.016 0.152
#> TCGA-02-0028-01A-01 1 0.0000 0.58856 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.5689 0.58121 0.780 0.036 0.184
#> TCGA-02-0047-01A-01 3 0.9585 0.34074 0.332 0.212 0.456
#> TCGA-02-0048-01A-01 1 0.4642 0.60865 0.856 0.060 0.084
#> TCGA-02-0060-01A-01 1 0.8169 0.26730 0.536 0.076 0.388
#> TCGA-02-0069-01A-01 1 0.0000 0.58856 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.6319 0.53985 0.732 0.040 0.228
#> TCGA-02-0080-01A-01 1 0.5098 0.43839 0.752 0.000 0.248
#> TCGA-02-0084-01A-03 3 0.8731 0.34288 0.352 0.120 0.528
#> TCGA-02-0087-01A-01 3 0.8731 0.34288 0.352 0.120 0.528
#> TCGA-02-0104-01A-01 1 0.0000 0.58856 1.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.58856 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.58856 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.8351 0.49605 0.604 0.124 0.272
#> TCGA-02-0325-01A-01 1 0.8351 0.49605 0.604 0.124 0.272
#> TCGA-02-0338-01A-01 1 0.0000 0.58856 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.58856 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.5098 0.43839 0.752 0.000 0.248
#> TCGA-02-0439-01A-01 1 0.8228 -0.00828 0.512 0.076 0.412
#> TCGA-02-0440-01A-01 1 0.6984 0.44717 0.656 0.040 0.304
#> TCGA-02-0446-01A-01 3 0.9598 0.31376 0.348 0.208 0.444
#> TCGA-06-0128-01A-01 1 0.5690 0.38475 0.708 0.004 0.288
#> TCGA-06-0129-01A-01 1 0.5404 0.42922 0.740 0.004 0.256
#> TCGA-06-0146-01A-01 1 0.6448 0.30260 0.656 0.016 0.328
#> TCGA-06-0156-01A-01 3 0.9678 0.35739 0.328 0.228 0.444
#> TCGA-06-0166-01A-01 1 0.9098 0.12924 0.492 0.148 0.360
#> TCGA-06-0174-01A-01 1 0.5689 0.58121 0.780 0.036 0.184
#> TCGA-06-0177-01A-01 1 0.6443 0.52872 0.720 0.040 0.240
#> TCGA-06-0238-01A-02 1 0.6665 0.48731 0.688 0.036 0.276
#> TCGA-06-0241-01A-02 1 0.3325 0.60207 0.904 0.020 0.076
#> TCGA-06-0410-01A-01 1 0.3325 0.60207 0.904 0.020 0.076
#> TCGA-06-0413-01A-01 1 0.0237 0.58907 0.996 0.000 0.004
#> TCGA-06-0414-01A-01 1 0.5559 0.56839 0.780 0.028 0.192
#> TCGA-06-0646-01A-01 3 0.9678 0.35739 0.328 0.228 0.444
#> TCGA-06-0648-01A-01 1 0.4539 0.56421 0.836 0.016 0.148
#> TCGA-08-0245-01A-01 1 0.2846 0.60415 0.924 0.020 0.056
#> TCGA-08-0344-01A-01 1 0.0592 0.58750 0.988 0.000 0.012
#> TCGA-08-0347-01A-01 3 0.9598 0.31376 0.348 0.208 0.444
#> TCGA-08-0348-01A-01 1 0.7920 0.28293 0.572 0.068 0.360
#> TCGA-08-0350-01A-01 1 0.6396 0.31192 0.664 0.016 0.320
#> TCGA-08-0353-01A-01 1 0.6705 0.58614 0.748 0.144 0.108
#> TCGA-08-0359-01A-01 3 0.9432 0.27735 0.372 0.180 0.448
#> TCGA-08-0385-01A-01 1 0.2774 0.57937 0.920 0.008 0.072
#> TCGA-08-0517-01A-01 1 0.3921 0.59853 0.884 0.036 0.080
#> TCGA-08-0524-01A-01 1 0.0000 0.58856 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.4609 0.58604 0.844 0.028 0.128
#> TCGA-12-0618-01A-01 1 0.4539 0.56421 0.836 0.016 0.148
#> TCGA-02-0089-01A-01 2 0.7013 0.09797 0.020 0.548 0.432
#> TCGA-02-0113-01A-01 3 0.9744 -0.11772 0.336 0.236 0.428
#> TCGA-02-0115-01A-01 3 0.5905 0.43003 0.000 0.352 0.648
#> TCGA-02-0451-01A-01 3 0.7184 0.17570 0.024 0.472 0.504
#> TCGA-06-0132-01A-02 3 0.5882 0.43542 0.000 0.348 0.652
#> TCGA-06-0133-01A-02 3 0.5695 0.61668 0.076 0.120 0.804
#> TCGA-06-0138-01A-02 3 0.7446 0.57335 0.076 0.260 0.664
#> TCGA-06-0160-01A-01 3 0.4121 0.51903 0.168 0.000 0.832
#> TCGA-06-0162-01A-01 3 0.5053 0.58782 0.024 0.164 0.812
#> TCGA-06-0167-01A-01 3 0.4121 0.51903 0.168 0.000 0.832
#> TCGA-06-0171-01A-02 3 0.7411 0.57738 0.076 0.256 0.668
#> TCGA-06-0173-01A-01 2 0.7607 0.21107 0.052 0.584 0.364
#> TCGA-06-0179-01A-02 3 0.5882 0.43542 0.000 0.348 0.652
#> TCGA-06-0182-01A-01 3 0.8167 0.37293 0.168 0.188 0.644
#> TCGA-06-0185-01A-01 3 0.9145 0.24752 0.216 0.240 0.544
#> TCGA-06-0195-01B-01 3 0.5780 0.59306 0.120 0.080 0.800
#> TCGA-06-0208-01B-01 3 0.5954 0.61311 0.092 0.116 0.792
#> TCGA-06-0214-01A-02 3 0.7382 0.21838 0.032 0.456 0.512
#> TCGA-06-0219-01A-01 3 0.5576 0.60871 0.084 0.104 0.812
#> TCGA-06-0221-01A-01 3 0.6148 0.58095 0.148 0.076 0.776
#> TCGA-06-0237-01A-02 3 0.6144 0.61932 0.088 0.132 0.780
#> TCGA-06-0240-01A-02 3 0.4121 0.51903 0.168 0.000 0.832
#> TCGA-08-0349-01A-01 3 0.8016 0.56847 0.108 0.260 0.632
#> TCGA-08-0380-01A-01 3 0.5988 0.40424 0.000 0.368 0.632
#> TCGA-08-0386-01A-01 3 0.9599 -0.19837 0.388 0.200 0.412
#> TCGA-08-0520-01A-01 3 0.9339 0.07900 0.316 0.188 0.496
#> TCGA-02-0007-01A-01 1 0.9278 0.46992 0.516 0.196 0.288
#> TCGA-02-0009-01A-01 1 0.9084 0.52212 0.552 0.232 0.216
#> TCGA-02-0016-01A-01 1 0.9086 0.52197 0.552 0.228 0.220
#> TCGA-02-0021-01A-01 1 0.9084 0.52212 0.552 0.232 0.216
#> TCGA-02-0023-01B-01 2 0.9666 -0.04854 0.324 0.448 0.228
#> TCGA-02-0027-01A-01 1 0.8649 0.29146 0.528 0.112 0.360
#> TCGA-02-0038-01A-01 2 0.7379 0.23040 0.040 0.584 0.376
#> TCGA-02-0043-01A-01 1 0.9084 0.52212 0.552 0.232 0.216
#> TCGA-02-0070-01A-01 2 0.4295 0.69299 0.032 0.864 0.104
#> TCGA-02-0102-01A-01 1 0.9092 0.51074 0.548 0.252 0.200
#> TCGA-02-0260-01A-03 1 0.8787 0.54179 0.584 0.188 0.228
#> TCGA-02-0269-01B-01 1 0.8787 0.54179 0.584 0.188 0.228
#> TCGA-02-0285-01A-01 1 0.9391 0.46127 0.504 0.284 0.212
#> TCGA-02-0289-01A-01 1 0.9151 0.51713 0.544 0.228 0.228
#> TCGA-02-0290-01A-01 1 0.9379 0.47375 0.508 0.276 0.216
#> TCGA-02-0317-01A-01 1 0.8977 0.52127 0.560 0.188 0.252
#> TCGA-02-0333-01A-02 1 0.8787 0.54179 0.584 0.188 0.228
#> TCGA-02-0422-01A-01 1 0.9830 0.30203 0.408 0.340 0.252
#> TCGA-02-0430-01A-01 1 0.9391 0.46127 0.504 0.284 0.212
#> TCGA-06-0125-01A-01 1 0.9084 0.52212 0.552 0.232 0.216
#> TCGA-06-0126-01A-01 1 0.9049 0.52428 0.556 0.232 0.212
#> TCGA-06-0137-01A-03 1 0.9014 0.52450 0.560 0.232 0.208
#> TCGA-06-0145-01A-04 1 0.9638 0.39408 0.460 0.308 0.232
#> TCGA-06-0148-01A-01 1 0.9283 0.49230 0.524 0.260 0.216
#> TCGA-06-0187-01A-01 2 0.9695 -0.24924 0.384 0.400 0.216
#> TCGA-06-0211-01B-01 1 0.9213 0.50892 0.536 0.236 0.228
#> TCGA-06-0402-01A-01 1 0.9084 0.52212 0.552 0.232 0.216
#> TCGA-08-0246-01A-01 2 0.9367 0.14474 0.292 0.504 0.204
#> TCGA-08-0354-01A-01 2 0.9615 -0.04478 0.324 0.456 0.220
#> TCGA-08-0355-01A-01 2 0.9347 0.15892 0.288 0.508 0.204
#> TCGA-08-0357-01A-01 1 0.9830 0.30203 0.408 0.340 0.252
#> TCGA-08-0358-01A-01 1 0.8977 0.52127 0.560 0.188 0.252
#> TCGA-08-0375-01A-01 1 0.8799 0.54218 0.584 0.196 0.220
#> TCGA-08-0511-01A-01 2 0.9651 -0.26417 0.392 0.400 0.208
#> TCGA-08-0514-01A-01 2 0.9623 -0.23813 0.384 0.412 0.204
#> TCGA-08-0518-01A-01 1 0.9170 0.50936 0.540 0.248 0.212
#> TCGA-08-0529-01A-02 1 0.9391 0.46127 0.504 0.284 0.212
#> TCGA-08-0531-01A-01 1 0.9145 0.51464 0.544 0.240 0.216
#> TCGA-02-0057-01A-01 2 0.6745 0.12041 0.012 0.560 0.428
#> TCGA-02-0004-01A-01 2 0.0237 0.76135 0.000 0.996 0.004
#> TCGA-02-0006-01B-01 2 0.6758 0.30722 0.020 0.620 0.360
#> TCGA-02-0025-01A-01 2 0.1289 0.76041 0.000 0.968 0.032
#> TCGA-02-0033-01A-01 2 0.0000 0.76246 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0747 0.76394 0.000 0.984 0.016
#> TCGA-02-0039-01A-01 2 0.3482 0.67747 0.000 0.872 0.128
#> TCGA-02-0051-01A-01 2 0.0747 0.76190 0.000 0.984 0.016
#> TCGA-02-0054-01A-01 2 0.6019 0.46989 0.012 0.700 0.288
#> TCGA-02-0055-01A-01 2 0.0237 0.76135 0.000 0.996 0.004
#> TCGA-02-0059-01A-01 2 0.0000 0.76246 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 2 0.0592 0.76394 0.000 0.988 0.012
#> TCGA-02-0075-01A-01 2 0.0892 0.76274 0.000 0.980 0.020
#> TCGA-02-0079-01A-03 2 0.6852 0.42984 0.036 0.664 0.300
#> TCGA-02-0085-01A-01 2 0.5982 0.38031 0.004 0.668 0.328
#> TCGA-02-0086-01A-01 2 0.0892 0.76274 0.000 0.980 0.020
#> TCGA-02-0099-01A-01 2 0.5115 0.56694 0.004 0.768 0.228
#> TCGA-02-0106-01A-01 2 0.0424 0.76308 0.000 0.992 0.008
#> TCGA-02-0107-01A-01 2 0.0424 0.76316 0.000 0.992 0.008
#> TCGA-02-0111-01A-01 2 0.0424 0.76316 0.000 0.992 0.008
#> TCGA-02-0326-01A-01 3 0.9581 0.35448 0.252 0.268 0.480
#> TCGA-02-0337-01A-01 2 0.6082 0.44253 0.012 0.692 0.296
#> TCGA-06-0122-01A-01 2 0.3530 0.72534 0.032 0.900 0.068
#> TCGA-06-0124-01A-01 2 0.1031 0.76257 0.000 0.976 0.024
#> TCGA-06-0130-01A-01 2 0.0237 0.76135 0.000 0.996 0.004
#> TCGA-06-0139-01A-01 2 0.0237 0.76135 0.000 0.996 0.004
#> TCGA-06-0143-01A-01 2 0.3530 0.72154 0.032 0.900 0.068
#> TCGA-06-0147-01A-01 2 0.0237 0.76135 0.000 0.996 0.004
#> TCGA-06-0149-01A-05 2 0.8842 0.30134 0.208 0.580 0.212
#> TCGA-06-0152-01A-02 2 0.9544 -0.04929 0.328 0.464 0.208
#> TCGA-06-0154-01A-02 2 0.1163 0.76204 0.000 0.972 0.028
#> TCGA-06-0164-01A-01 2 0.0424 0.76316 0.000 0.992 0.008
#> TCGA-06-0175-01A-01 2 0.5356 0.62011 0.020 0.784 0.196
#> TCGA-06-0176-01A-03 2 0.0237 0.76302 0.000 0.996 0.004
#> TCGA-06-0184-01A-01 2 0.6274 0.03798 0.000 0.544 0.456
#> TCGA-06-0189-01A-05 2 0.0000 0.76246 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 2 0.1031 0.76257 0.000 0.976 0.024
#> TCGA-06-0194-01A-01 2 0.1620 0.75903 0.012 0.964 0.024
#> TCGA-06-0197-01A-02 2 0.0000 0.76246 0.000 1.000 0.000
#> TCGA-06-0210-01A-01 2 0.3530 0.72344 0.032 0.900 0.068
#> TCGA-06-0397-01A-01 2 0.0747 0.76190 0.000 0.984 0.016
#> TCGA-06-0409-01A-02 2 0.0424 0.76316 0.000 0.992 0.008
#> TCGA-06-0412-01A-01 2 0.3530 0.72344 0.032 0.900 0.068
#> TCGA-06-0644-01A-02 2 0.0424 0.76308 0.000 0.992 0.008
#> TCGA-06-0645-01A-01 2 0.1031 0.76438 0.000 0.976 0.024
#> TCGA-08-0346-01A-01 2 0.2187 0.75089 0.024 0.948 0.028
#> TCGA-08-0352-01A-01 2 0.5634 0.64928 0.056 0.800 0.144
#> TCGA-08-0360-01A-01 2 0.0747 0.76394 0.000 0.984 0.016
#> TCGA-08-0390-01A-01 2 0.5733 0.39004 0.000 0.676 0.324
#> TCGA-08-0392-01A-01 2 0.0747 0.76190 0.000 0.984 0.016
#> TCGA-08-0509-01A-01 2 0.1753 0.74237 0.000 0.952 0.048
#> TCGA-08-0510-01A-01 2 0.1529 0.75803 0.000 0.960 0.040
#> TCGA-08-0512-01A-01 2 0.0424 0.76440 0.000 0.992 0.008
#> TCGA-08-0522-01A-01 2 0.0592 0.76282 0.000 0.988 0.012
#> TCGA-12-0619-01A-01 2 0.0000 0.76246 0.000 1.000 0.000
#> TCGA-12-0620-01A-01 2 0.7458 0.44601 0.196 0.692 0.112
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.6830 0.63541 0.616 0.004 0.220 0.160
#> TCGA-02-0010-01A-01 1 0.0592 0.71418 0.984 0.000 0.016 0.000
#> TCGA-02-0011-01B-01 1 0.7293 0.49170 0.496 0.000 0.164 0.340
#> TCGA-02-0014-01A-01 1 0.0592 0.71418 0.984 0.000 0.016 0.000
#> TCGA-02-0024-01B-01 1 0.0779 0.71479 0.980 0.000 0.016 0.004
#> TCGA-02-0026-01B-01 1 0.6685 0.65006 0.616 0.000 0.224 0.160
#> TCGA-02-0028-01A-01 1 0.0592 0.71418 0.984 0.000 0.016 0.000
#> TCGA-02-0046-01A-01 1 0.6830 0.63541 0.616 0.004 0.220 0.160
#> TCGA-02-0047-01A-01 4 0.9158 0.41895 0.164 0.128 0.260 0.448
#> TCGA-02-0048-01A-01 1 0.5445 0.66354 0.708 0.004 0.240 0.048
#> TCGA-02-0060-01A-01 4 0.8332 -0.10102 0.300 0.016 0.296 0.388
#> TCGA-02-0069-01A-01 1 0.0592 0.71418 0.984 0.000 0.016 0.000
#> TCGA-02-0074-01A-01 1 0.7469 0.56245 0.532 0.004 0.240 0.224
#> TCGA-02-0080-01A-01 1 0.6779 0.55189 0.560 0.000 0.116 0.324
#> TCGA-02-0084-01A-03 4 0.7265 0.39577 0.096 0.036 0.272 0.596
#> TCGA-02-0087-01A-01 4 0.7265 0.39577 0.096 0.036 0.272 0.596
#> TCGA-02-0104-01A-01 1 0.0592 0.71418 0.984 0.000 0.016 0.000
#> TCGA-02-0114-01A-01 1 0.0592 0.71418 0.984 0.000 0.016 0.000
#> TCGA-02-0281-01A-01 1 0.0592 0.71418 0.984 0.000 0.016 0.000
#> TCGA-02-0321-01A-01 3 0.7925 0.04866 0.256 0.016 0.500 0.228
#> TCGA-02-0325-01A-01 3 0.7925 0.04866 0.256 0.016 0.500 0.228
#> TCGA-02-0338-01A-01 1 0.0592 0.71418 0.984 0.000 0.016 0.000
#> TCGA-02-0339-01A-01 1 0.0592 0.71418 0.984 0.000 0.016 0.000
#> TCGA-02-0432-01A-02 1 0.6779 0.55189 0.560 0.000 0.116 0.324
#> TCGA-02-0439-01A-01 4 0.8458 0.07538 0.280 0.040 0.216 0.464
#> TCGA-02-0440-01A-01 1 0.7948 0.37481 0.424 0.004 0.280 0.292
#> TCGA-02-0446-01A-01 4 0.9252 0.39321 0.180 0.128 0.256 0.436
#> TCGA-06-0128-01A-01 1 0.6685 0.54505 0.568 0.000 0.108 0.324
#> TCGA-06-0129-01A-01 1 0.6415 0.59460 0.612 0.000 0.100 0.288
#> TCGA-06-0146-01A-01 1 0.7281 0.42132 0.468 0.000 0.152 0.380
#> TCGA-06-0156-01A-01 4 0.9348 0.42370 0.172 0.152 0.244 0.432
#> TCGA-06-0166-01A-01 4 0.9234 0.03607 0.292 0.076 0.284 0.348
#> TCGA-06-0174-01A-01 1 0.6830 0.63541 0.616 0.004 0.220 0.160
#> TCGA-06-0177-01A-01 1 0.7686 0.51516 0.492 0.004 0.260 0.244
#> TCGA-06-0238-01A-02 1 0.7871 0.45012 0.448 0.004 0.268 0.280
#> TCGA-06-0241-01A-02 1 0.4569 0.71862 0.800 0.004 0.144 0.052
#> TCGA-06-0410-01A-01 1 0.4569 0.71862 0.800 0.004 0.144 0.052
#> TCGA-06-0413-01A-01 1 0.0779 0.71479 0.980 0.000 0.016 0.004
#> TCGA-06-0414-01A-01 1 0.6863 0.63518 0.616 0.004 0.196 0.184
#> TCGA-06-0646-01A-01 4 0.9348 0.42370 0.172 0.152 0.244 0.432
#> TCGA-06-0648-01A-01 1 0.6646 0.65826 0.620 0.000 0.224 0.156
#> TCGA-08-0245-01A-01 1 0.3877 0.72190 0.840 0.004 0.124 0.032
#> TCGA-08-0344-01A-01 1 0.2623 0.71811 0.908 0.000 0.064 0.028
#> TCGA-08-0347-01A-01 4 0.9252 0.39321 0.180 0.128 0.256 0.436
#> TCGA-08-0348-01A-01 4 0.8436 -0.20588 0.348 0.020 0.280 0.352
#> TCGA-08-0350-01A-01 1 0.7310 0.44121 0.480 0.000 0.160 0.360
#> TCGA-08-0353-01A-01 3 0.6035 0.20914 0.372 0.020 0.588 0.020
#> TCGA-08-0359-01A-01 4 0.9134 0.36048 0.196 0.104 0.260 0.440
#> TCGA-08-0385-01A-01 1 0.5032 0.70619 0.764 0.000 0.156 0.080
#> TCGA-08-0517-01A-01 1 0.4786 0.71632 0.800 0.012 0.128 0.060
#> TCGA-08-0524-01A-01 1 0.0592 0.71418 0.984 0.000 0.016 0.000
#> TCGA-12-0616-01A-01 1 0.6127 0.67348 0.664 0.000 0.228 0.108
#> TCGA-12-0618-01A-01 1 0.6646 0.65826 0.620 0.000 0.224 0.156
#> TCGA-02-0089-01A-01 4 0.7169 0.07171 0.004 0.424 0.116 0.456
#> TCGA-02-0113-01A-01 3 0.5835 0.55316 0.008 0.060 0.688 0.244
#> TCGA-02-0115-01A-01 4 0.4936 0.49240 0.000 0.280 0.020 0.700
#> TCGA-02-0451-01A-01 4 0.6990 0.30070 0.004 0.364 0.108 0.524
#> TCGA-06-0132-01A-02 4 0.4831 0.49434 0.000 0.280 0.016 0.704
#> TCGA-06-0133-01A-02 4 0.4336 0.58984 0.008 0.064 0.100 0.828
#> TCGA-06-0138-01A-02 4 0.6737 0.60571 0.032 0.184 0.112 0.672
#> TCGA-06-0160-01A-01 4 0.1867 0.48202 0.072 0.000 0.000 0.928
#> TCGA-06-0162-01A-01 4 0.2867 0.59267 0.000 0.104 0.012 0.884
#> TCGA-06-0167-01A-01 4 0.1867 0.48202 0.072 0.000 0.000 0.928
#> TCGA-06-0171-01A-02 4 0.6699 0.60923 0.032 0.180 0.112 0.676
#> TCGA-06-0173-01A-01 2 0.7713 0.03901 0.016 0.464 0.144 0.376
#> TCGA-06-0179-01A-02 4 0.4831 0.49434 0.000 0.280 0.016 0.704
#> TCGA-06-0182-01A-01 4 0.6275 -0.05457 0.000 0.056 0.460 0.484
#> TCGA-06-0185-01A-01 3 0.6669 0.24916 0.004 0.076 0.520 0.400
#> TCGA-06-0195-01B-01 4 0.4174 0.56510 0.036 0.052 0.060 0.852
#> TCGA-06-0208-01B-01 4 0.4551 0.58588 0.008 0.060 0.120 0.812
#> TCGA-06-0214-01A-02 4 0.7289 0.33161 0.012 0.352 0.116 0.520
#> TCGA-06-0219-01A-01 4 0.3648 0.57999 0.008 0.056 0.068 0.868
#> TCGA-06-0221-01A-01 4 0.4670 0.54944 0.064 0.052 0.056 0.828
#> TCGA-06-0237-01A-02 4 0.4725 0.59531 0.008 0.076 0.112 0.804
#> TCGA-06-0240-01A-02 4 0.1867 0.48202 0.072 0.000 0.000 0.928
#> TCGA-08-0349-01A-01 4 0.6748 0.55137 0.012 0.156 0.184 0.648
#> TCGA-08-0380-01A-01 4 0.5062 0.46719 0.000 0.300 0.020 0.680
#> TCGA-08-0386-01A-01 3 0.6353 0.53783 0.048 0.036 0.668 0.248
#> TCGA-08-0520-01A-01 3 0.6544 0.33240 0.016 0.052 0.572 0.360
#> TCGA-02-0007-01A-01 3 0.4867 0.69185 0.064 0.020 0.804 0.112
#> TCGA-02-0009-01A-01 3 0.1724 0.76970 0.032 0.020 0.948 0.000
#> TCGA-02-0016-01A-01 3 0.2719 0.76486 0.040 0.020 0.916 0.024
#> TCGA-02-0021-01A-01 3 0.1724 0.76970 0.032 0.020 0.948 0.000
#> TCGA-02-0023-01B-01 3 0.5711 0.57297 0.004 0.220 0.704 0.072
#> TCGA-02-0027-01A-01 3 0.8398 -0.15134 0.216 0.028 0.408 0.348
#> TCGA-02-0038-01A-01 2 0.7690 0.00936 0.004 0.436 0.188 0.372
#> TCGA-02-0043-01A-01 3 0.1706 0.76874 0.036 0.016 0.948 0.000
#> TCGA-02-0070-01A-01 2 0.5088 0.63480 0.000 0.688 0.288 0.024
#> TCGA-02-0102-01A-01 3 0.2317 0.77174 0.036 0.032 0.928 0.004
#> TCGA-02-0260-01A-03 3 0.1557 0.74815 0.056 0.000 0.944 0.000
#> TCGA-02-0269-01B-01 3 0.1557 0.74815 0.056 0.000 0.944 0.000
#> TCGA-02-0285-01A-01 3 0.3204 0.76412 0.028 0.064 0.892 0.016
#> TCGA-02-0289-01A-01 3 0.1284 0.76607 0.024 0.012 0.964 0.000
#> TCGA-02-0290-01A-01 3 0.2413 0.76543 0.020 0.064 0.916 0.000
#> TCGA-02-0317-01A-01 3 0.2466 0.73750 0.056 0.000 0.916 0.028
#> TCGA-02-0333-01A-02 3 0.1557 0.74815 0.056 0.000 0.944 0.000
#> TCGA-02-0422-01A-01 3 0.4411 0.71113 0.012 0.112 0.824 0.052
#> TCGA-02-0430-01A-01 3 0.3204 0.76412 0.028 0.064 0.892 0.016
#> TCGA-06-0125-01A-01 3 0.1724 0.76970 0.032 0.020 0.948 0.000
#> TCGA-06-0126-01A-01 3 0.1820 0.76974 0.036 0.020 0.944 0.000
#> TCGA-06-0137-01A-03 3 0.2284 0.76808 0.036 0.020 0.932 0.012
#> TCGA-06-0145-01A-04 3 0.3540 0.74075 0.012 0.084 0.872 0.032
#> TCGA-06-0148-01A-01 3 0.2089 0.76969 0.020 0.048 0.932 0.000
#> TCGA-06-0187-01A-01 3 0.5227 0.65128 0.008 0.176 0.756 0.060
#> TCGA-06-0211-01B-01 3 0.2310 0.77111 0.032 0.020 0.932 0.016
#> TCGA-06-0402-01A-01 3 0.1706 0.76874 0.036 0.016 0.948 0.000
#> TCGA-08-0246-01A-01 3 0.6514 0.46058 0.004 0.284 0.616 0.096
#> TCGA-08-0354-01A-01 3 0.5312 0.58175 0.000 0.236 0.712 0.052
#> TCGA-08-0355-01A-01 3 0.6113 0.47742 0.000 0.284 0.636 0.080
#> TCGA-08-0357-01A-01 3 0.4411 0.71113 0.012 0.112 0.824 0.052
#> TCGA-08-0358-01A-01 3 0.2466 0.73750 0.056 0.000 0.916 0.028
#> TCGA-08-0375-01A-01 3 0.1557 0.74893 0.056 0.000 0.944 0.000
#> TCGA-08-0511-01A-01 3 0.5196 0.66172 0.008 0.160 0.764 0.068
#> TCGA-08-0514-01A-01 3 0.5195 0.65033 0.008 0.180 0.756 0.056
#> TCGA-08-0518-01A-01 3 0.1936 0.77193 0.028 0.032 0.940 0.000
#> TCGA-08-0529-01A-02 3 0.3204 0.76412 0.028 0.064 0.892 0.016
#> TCGA-08-0531-01A-01 3 0.1733 0.77134 0.028 0.024 0.948 0.000
#> TCGA-02-0057-01A-01 4 0.6969 0.04022 0.000 0.436 0.112 0.452
#> TCGA-02-0004-01A-01 2 0.0376 0.80003 0.004 0.992 0.000 0.004
#> TCGA-02-0006-01B-01 2 0.7228 0.14876 0.004 0.492 0.128 0.376
#> TCGA-02-0025-01A-01 2 0.1847 0.79396 0.004 0.940 0.052 0.004
#> TCGA-02-0033-01A-01 2 0.0188 0.80372 0.000 0.996 0.004 0.000
#> TCGA-02-0034-01A-01 2 0.2207 0.81014 0.004 0.928 0.056 0.012
#> TCGA-02-0039-01A-01 2 0.5186 0.69396 0.000 0.752 0.084 0.164
#> TCGA-02-0051-01A-01 2 0.1082 0.80152 0.004 0.972 0.020 0.004
#> TCGA-02-0054-01A-01 2 0.6865 0.39048 0.004 0.576 0.116 0.304
#> TCGA-02-0055-01A-01 2 0.0376 0.80003 0.004 0.992 0.000 0.004
#> TCGA-02-0059-01A-01 2 0.0376 0.80221 0.004 0.992 0.004 0.000
#> TCGA-02-0064-01A-01 2 0.1389 0.81024 0.000 0.952 0.048 0.000
#> TCGA-02-0075-01A-01 2 0.2973 0.79829 0.000 0.884 0.096 0.020
#> TCGA-02-0079-01A-03 2 0.7325 0.29925 0.004 0.536 0.168 0.292
#> TCGA-02-0085-01A-01 2 0.6688 0.26808 0.000 0.536 0.096 0.368
#> TCGA-02-0086-01A-01 2 0.2949 0.79993 0.000 0.888 0.088 0.024
#> TCGA-02-0099-01A-01 2 0.6167 0.52797 0.000 0.648 0.096 0.256
#> TCGA-02-0106-01A-01 2 0.0967 0.80199 0.004 0.976 0.016 0.004
#> TCGA-02-0107-01A-01 2 0.0336 0.80581 0.000 0.992 0.008 0.000
#> TCGA-02-0111-01A-01 2 0.0524 0.80688 0.000 0.988 0.008 0.004
#> TCGA-02-0326-01A-01 3 0.7825 -0.08828 0.028 0.124 0.452 0.396
#> TCGA-02-0337-01A-01 2 0.7050 0.36010 0.008 0.572 0.124 0.296
#> TCGA-06-0122-01A-01 2 0.4939 0.70762 0.000 0.740 0.220 0.040
#> TCGA-06-0124-01A-01 2 0.3278 0.79039 0.000 0.864 0.116 0.020
#> TCGA-06-0130-01A-01 2 0.0376 0.80003 0.004 0.992 0.000 0.004
#> TCGA-06-0139-01A-01 2 0.0000 0.80217 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 2 0.4818 0.71349 0.000 0.748 0.216 0.036
#> TCGA-06-0147-01A-01 2 0.0000 0.80217 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.6971 0.17202 0.000 0.372 0.508 0.120
#> TCGA-06-0152-01A-02 3 0.5302 0.57571 0.004 0.232 0.720 0.044
#> TCGA-06-0154-01A-02 2 0.3653 0.78269 0.000 0.844 0.128 0.028
#> TCGA-06-0164-01A-01 2 0.1042 0.80753 0.000 0.972 0.008 0.020
#> TCGA-06-0175-01A-01 2 0.6639 0.58260 0.004 0.640 0.196 0.160
#> TCGA-06-0176-01A-03 2 0.0712 0.80158 0.004 0.984 0.008 0.004
#> TCGA-06-0184-01A-01 4 0.6451 0.02509 0.000 0.456 0.068 0.476
#> TCGA-06-0189-01A-05 2 0.0712 0.80561 0.004 0.984 0.008 0.004
#> TCGA-06-0190-01A-01 2 0.3278 0.79039 0.000 0.864 0.116 0.020
#> TCGA-06-0194-01A-01 2 0.3447 0.78617 0.000 0.852 0.128 0.020
#> TCGA-06-0197-01A-02 2 0.0188 0.80372 0.000 0.996 0.004 0.000
#> TCGA-06-0210-01A-01 2 0.4728 0.71599 0.000 0.752 0.216 0.032
#> TCGA-06-0397-01A-01 2 0.1661 0.80691 0.000 0.944 0.052 0.004
#> TCGA-06-0409-01A-02 2 0.1109 0.80995 0.000 0.968 0.028 0.004
#> TCGA-06-0412-01A-01 2 0.4728 0.71599 0.000 0.752 0.216 0.032
#> TCGA-06-0644-01A-02 2 0.0844 0.80161 0.004 0.980 0.012 0.004
#> TCGA-06-0645-01A-01 2 0.3243 0.79620 0.000 0.876 0.088 0.036
#> TCGA-08-0346-01A-01 2 0.3711 0.77697 0.000 0.836 0.140 0.024
#> TCGA-08-0352-01A-01 2 0.6098 0.53979 0.000 0.616 0.316 0.068
#> TCGA-08-0360-01A-01 2 0.2256 0.80806 0.000 0.924 0.056 0.020
#> TCGA-08-0390-01A-01 2 0.5793 0.36508 0.000 0.600 0.040 0.360
#> TCGA-08-0392-01A-01 2 0.1082 0.80152 0.004 0.972 0.020 0.004
#> TCGA-08-0509-01A-01 2 0.2699 0.79215 0.000 0.904 0.028 0.068
#> TCGA-08-0510-01A-01 2 0.4008 0.76919 0.000 0.820 0.148 0.032
#> TCGA-08-0512-01A-01 2 0.1557 0.81035 0.000 0.944 0.056 0.000
#> TCGA-08-0522-01A-01 2 0.0967 0.80187 0.004 0.976 0.016 0.004
#> TCGA-12-0619-01A-01 2 0.0712 0.80475 0.004 0.984 0.004 0.008
#> TCGA-12-0620-01A-01 2 0.6538 0.30716 0.000 0.528 0.392 0.080
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.6685 0.45375 0.592 0.000 0.212 0.056 0.140
#> TCGA-02-0010-01A-01 1 0.0000 0.61641 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 5 0.6597 -0.07782 0.400 0.000 0.124 0.020 0.456
#> TCGA-02-0014-01A-01 1 0.0000 0.61641 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0162 0.61646 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0026-01B-01 1 0.6288 0.42997 0.572 0.000 0.192 0.008 0.228
#> TCGA-02-0028-01A-01 1 0.0000 0.61641 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.6685 0.45375 0.592 0.000 0.212 0.056 0.140
#> TCGA-02-0047-01A-01 4 0.8411 0.07148 0.120 0.028 0.204 0.456 0.192
#> TCGA-02-0048-01A-01 1 0.5107 0.51203 0.696 0.004 0.236 0.012 0.052
#> TCGA-02-0060-01A-01 5 0.8566 0.14964 0.228 0.000 0.252 0.220 0.300
#> TCGA-02-0069-01A-01 1 0.0000 0.61641 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.7450 0.32982 0.496 0.000 0.208 0.072 0.224
#> TCGA-02-0080-01A-01 1 0.5935 0.12427 0.484 0.000 0.064 0.016 0.436
#> TCGA-02-0084-01A-03 5 0.6219 0.41751 0.008 0.004 0.172 0.216 0.600
#> TCGA-02-0087-01A-01 5 0.6219 0.41751 0.008 0.004 0.172 0.216 0.600
#> TCGA-02-0104-01A-01 1 0.0000 0.61641 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.61641 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.61641 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.7521 -0.04151 0.196 0.000 0.496 0.084 0.224
#> TCGA-02-0325-01A-01 3 0.7521 -0.04151 0.196 0.000 0.496 0.084 0.224
#> TCGA-02-0338-01A-01 1 0.0000 0.61641 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.61641 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.5935 0.12427 0.484 0.000 0.064 0.016 0.436
#> TCGA-02-0439-01A-01 5 0.8303 0.30533 0.200 0.000 0.172 0.244 0.384
#> TCGA-02-0440-01A-01 1 0.8219 0.07610 0.368 0.000 0.248 0.124 0.260
#> TCGA-02-0446-01A-01 4 0.8544 0.03909 0.132 0.028 0.212 0.436 0.192
#> TCGA-06-0128-01A-01 1 0.6312 0.17987 0.500 0.000 0.068 0.036 0.396
#> TCGA-06-0129-01A-01 1 0.6048 0.27775 0.548 0.000 0.064 0.028 0.360
#> TCGA-06-0146-01A-01 5 0.6685 0.01751 0.384 0.000 0.104 0.036 0.476
#> TCGA-06-0156-01A-01 4 0.8553 0.09824 0.124 0.040 0.196 0.456 0.184
#> TCGA-06-0166-01A-01 4 0.9211 -0.29859 0.244 0.032 0.244 0.256 0.224
#> TCGA-06-0174-01A-01 1 0.6685 0.45375 0.592 0.000 0.212 0.056 0.140
#> TCGA-06-0177-01A-01 1 0.7688 0.24052 0.440 0.000 0.224 0.072 0.264
#> TCGA-06-0238-01A-02 1 0.7960 0.12218 0.388 0.000 0.220 0.092 0.300
#> TCGA-06-0241-01A-02 1 0.4380 0.59522 0.780 0.000 0.140 0.012 0.068
#> TCGA-06-0410-01A-01 1 0.4380 0.59522 0.780 0.000 0.140 0.012 0.068
#> TCGA-06-0413-01A-01 1 0.0162 0.61646 0.996 0.000 0.000 0.000 0.004
#> TCGA-06-0414-01A-01 1 0.6866 0.45023 0.588 0.000 0.188 0.076 0.148
#> TCGA-06-0646-01A-01 4 0.8553 0.09824 0.124 0.040 0.196 0.456 0.184
#> TCGA-06-0648-01A-01 1 0.6269 0.43966 0.576 0.000 0.196 0.008 0.220
#> TCGA-08-0245-01A-01 1 0.3389 0.60810 0.836 0.000 0.116 0.000 0.048
#> TCGA-08-0344-01A-01 1 0.2388 0.59533 0.900 0.000 0.028 0.000 0.072
#> TCGA-08-0347-01A-01 4 0.8544 0.03909 0.132 0.028 0.212 0.436 0.192
#> TCGA-08-0348-01A-01 1 0.8557 -0.14262 0.284 0.000 0.232 0.204 0.280
#> TCGA-08-0350-01A-01 5 0.6706 -0.04246 0.404 0.000 0.104 0.036 0.456
#> TCGA-08-0353-01A-01 3 0.4837 0.25087 0.348 0.000 0.624 0.008 0.020
#> TCGA-08-0359-01A-01 4 0.8317 -0.02400 0.128 0.012 0.208 0.432 0.220
#> TCGA-08-0385-01A-01 1 0.4648 0.53702 0.740 0.000 0.104 0.000 0.156
#> TCGA-08-0517-01A-01 1 0.4391 0.58879 0.788 0.000 0.136 0.032 0.044
#> TCGA-08-0524-01A-01 1 0.0000 0.61641 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.6073 0.48710 0.624 0.000 0.188 0.016 0.172
#> TCGA-12-0618-01A-01 1 0.6269 0.43966 0.576 0.000 0.196 0.008 0.220
#> TCGA-02-0089-01A-01 4 0.5463 0.44233 0.000 0.248 0.100 0.648 0.004
#> TCGA-02-0113-01A-01 3 0.5459 0.55731 0.000 0.028 0.672 0.240 0.060
#> TCGA-02-0115-01A-01 4 0.2408 0.49582 0.000 0.092 0.000 0.892 0.016
#> TCGA-02-0451-01A-01 4 0.5098 0.53367 0.000 0.180 0.092 0.716 0.012
#> TCGA-06-0132-01A-02 4 0.2505 0.49440 0.000 0.092 0.000 0.888 0.020
#> TCGA-06-0133-01A-02 4 0.5465 0.28052 0.000 0.020 0.084 0.680 0.216
#> TCGA-06-0138-01A-02 4 0.5844 0.44858 0.016 0.072 0.084 0.720 0.108
#> TCGA-06-0160-01A-01 5 0.4015 0.30825 0.000 0.000 0.000 0.348 0.652
#> TCGA-06-0162-01A-01 4 0.4109 0.33566 0.000 0.036 0.004 0.768 0.192
#> TCGA-06-0167-01A-01 5 0.4015 0.30825 0.000 0.000 0.000 0.348 0.652
#> TCGA-06-0171-01A-02 4 0.5833 0.44475 0.016 0.068 0.084 0.720 0.112
#> TCGA-06-0173-01A-01 4 0.6309 0.37473 0.004 0.284 0.128 0.572 0.012
#> TCGA-06-0179-01A-02 4 0.2505 0.49440 0.000 0.092 0.000 0.888 0.020
#> TCGA-06-0182-01A-01 3 0.6394 0.09623 0.000 0.028 0.448 0.440 0.084
#> TCGA-06-0185-01A-01 3 0.6275 0.29631 0.000 0.032 0.512 0.384 0.072
#> TCGA-06-0195-01B-01 4 0.5833 0.16486 0.012 0.020 0.052 0.624 0.292
#> TCGA-06-0208-01B-01 4 0.5681 0.26980 0.000 0.020 0.104 0.664 0.212
#> TCGA-06-0214-01A-02 4 0.5508 0.53183 0.004 0.172 0.096 0.704 0.024
#> TCGA-06-0219-01A-01 4 0.5415 0.21662 0.000 0.020 0.060 0.660 0.260
#> TCGA-06-0221-01A-01 4 0.6207 0.13001 0.032 0.020 0.048 0.604 0.296
#> TCGA-06-0237-01A-02 4 0.5576 0.29631 0.000 0.020 0.100 0.676 0.204
#> TCGA-06-0240-01A-02 5 0.4015 0.30825 0.000 0.000 0.000 0.348 0.652
#> TCGA-08-0349-01A-01 4 0.5894 0.41086 0.000 0.048 0.172 0.676 0.104
#> TCGA-08-0380-01A-01 4 0.3023 0.50465 0.000 0.112 0.004 0.860 0.024
#> TCGA-08-0386-01A-01 3 0.5928 0.54655 0.028 0.008 0.660 0.220 0.084
#> TCGA-08-0520-01A-01 3 0.6126 0.38153 0.000 0.020 0.564 0.324 0.092
#> TCGA-02-0007-01A-01 3 0.4357 0.67148 0.032 0.004 0.808 0.068 0.088
#> TCGA-02-0009-01A-01 3 0.0162 0.75000 0.000 0.000 0.996 0.004 0.000
#> TCGA-02-0016-01A-01 3 0.1173 0.74728 0.004 0.000 0.964 0.020 0.012
#> TCGA-02-0021-01A-01 3 0.0324 0.74957 0.000 0.000 0.992 0.004 0.004
#> TCGA-02-0023-01B-01 3 0.5667 0.56316 0.000 0.168 0.672 0.144 0.016
#> TCGA-02-0027-01A-01 3 0.8232 -0.28695 0.152 0.000 0.396 0.216 0.236
#> TCGA-02-0038-01A-01 4 0.6268 0.36623 0.000 0.268 0.176 0.552 0.004
#> TCGA-02-0043-01A-01 3 0.0451 0.74825 0.004 0.000 0.988 0.000 0.008
#> TCGA-02-0070-01A-01 2 0.6255 0.49636 0.000 0.568 0.260 0.164 0.008
#> TCGA-02-0102-01A-01 3 0.1143 0.75325 0.004 0.012 0.968 0.008 0.008
#> TCGA-02-0260-01A-03 3 0.2172 0.72509 0.016 0.000 0.908 0.000 0.076
#> TCGA-02-0269-01B-01 3 0.2172 0.72509 0.016 0.000 0.908 0.000 0.076
#> TCGA-02-0285-01A-01 3 0.1818 0.75134 0.000 0.024 0.932 0.044 0.000
#> TCGA-02-0289-01A-01 3 0.0963 0.74338 0.000 0.000 0.964 0.000 0.036
#> TCGA-02-0290-01A-01 3 0.2710 0.74443 0.000 0.064 0.892 0.008 0.036
#> TCGA-02-0317-01A-01 3 0.2982 0.70413 0.020 0.000 0.860 0.004 0.116
#> TCGA-02-0333-01A-02 3 0.2172 0.72509 0.016 0.000 0.908 0.000 0.076
#> TCGA-02-0422-01A-01 3 0.3799 0.70316 0.004 0.048 0.820 0.124 0.004
#> TCGA-02-0430-01A-01 3 0.1818 0.75134 0.000 0.024 0.932 0.044 0.000
#> TCGA-06-0125-01A-01 3 0.0162 0.75000 0.000 0.000 0.996 0.004 0.000
#> TCGA-06-0126-01A-01 3 0.0324 0.74996 0.004 0.000 0.992 0.004 0.000
#> TCGA-06-0137-01A-03 3 0.0693 0.74886 0.000 0.000 0.980 0.012 0.008
#> TCGA-06-0145-01A-04 3 0.2812 0.73489 0.000 0.024 0.876 0.096 0.004
#> TCGA-06-0148-01A-01 3 0.2381 0.74722 0.000 0.052 0.908 0.004 0.036
#> TCGA-06-0187-01A-01 3 0.4634 0.64775 0.000 0.100 0.752 0.144 0.004
#> TCGA-06-0211-01B-01 3 0.0865 0.75250 0.004 0.000 0.972 0.024 0.000
#> TCGA-06-0402-01A-01 3 0.0451 0.74825 0.004 0.000 0.988 0.000 0.008
#> TCGA-08-0246-01A-01 3 0.6192 0.44081 0.000 0.212 0.588 0.192 0.008
#> TCGA-08-0354-01A-01 3 0.5172 0.56457 0.000 0.216 0.692 0.084 0.008
#> TCGA-08-0355-01A-01 3 0.6064 0.45987 0.000 0.220 0.604 0.168 0.008
#> TCGA-08-0357-01A-01 3 0.3799 0.70316 0.004 0.048 0.820 0.124 0.004
#> TCGA-08-0358-01A-01 3 0.2982 0.70413 0.020 0.000 0.860 0.004 0.116
#> TCGA-08-0375-01A-01 3 0.2393 0.72234 0.016 0.000 0.900 0.004 0.080
#> TCGA-08-0511-01A-01 3 0.4592 0.65222 0.000 0.100 0.756 0.140 0.004
#> TCGA-08-0514-01A-01 3 0.4683 0.64238 0.000 0.104 0.748 0.144 0.004
#> TCGA-08-0518-01A-01 3 0.0833 0.75453 0.000 0.016 0.976 0.004 0.004
#> TCGA-08-0529-01A-02 3 0.1818 0.75134 0.000 0.024 0.932 0.044 0.000
#> TCGA-08-0531-01A-01 3 0.0613 0.75366 0.000 0.004 0.984 0.008 0.004
#> TCGA-02-0057-01A-01 4 0.5532 0.43176 0.000 0.256 0.092 0.644 0.008
#> TCGA-02-0004-01A-01 2 0.1106 0.75777 0.000 0.964 0.000 0.012 0.024
#> TCGA-02-0006-01B-01 4 0.5781 0.31849 0.000 0.308 0.116 0.576 0.000
#> TCGA-02-0025-01A-01 2 0.2694 0.71778 0.000 0.892 0.008 0.032 0.068
#> TCGA-02-0033-01A-01 2 0.1012 0.76678 0.000 0.968 0.000 0.012 0.020
#> TCGA-02-0034-01A-01 2 0.2605 0.77260 0.000 0.896 0.044 0.056 0.004
#> TCGA-02-0039-01A-01 2 0.5473 0.53521 0.000 0.628 0.056 0.300 0.016
#> TCGA-02-0051-01A-01 2 0.1934 0.74037 0.000 0.928 0.004 0.016 0.052
#> TCGA-02-0054-01A-01 4 0.6040 0.06313 0.000 0.396 0.104 0.496 0.004
#> TCGA-02-0055-01A-01 2 0.1106 0.75777 0.000 0.964 0.000 0.012 0.024
#> TCGA-02-0059-01A-01 2 0.0865 0.76279 0.000 0.972 0.000 0.004 0.024
#> TCGA-02-0064-01A-01 2 0.3423 0.75932 0.000 0.844 0.040 0.108 0.008
#> TCGA-02-0075-01A-01 2 0.4404 0.72939 0.000 0.776 0.080 0.136 0.008
#> TCGA-02-0079-01A-03 2 0.7443 -0.00798 0.000 0.416 0.096 0.380 0.108
#> TCGA-02-0085-01A-01 4 0.6072 0.15072 0.000 0.380 0.068 0.528 0.024
#> TCGA-02-0086-01A-01 2 0.4011 0.74785 0.000 0.808 0.072 0.112 0.008
#> TCGA-02-0099-01A-01 2 0.5745 0.15639 0.000 0.476 0.072 0.448 0.004
#> TCGA-02-0106-01A-01 2 0.1646 0.75263 0.000 0.944 0.004 0.020 0.032
#> TCGA-02-0107-01A-01 2 0.1857 0.77169 0.000 0.928 0.008 0.060 0.004
#> TCGA-02-0111-01A-01 2 0.1924 0.77211 0.000 0.924 0.008 0.064 0.004
#> TCGA-02-0326-01A-01 3 0.8084 -0.00627 0.004 0.076 0.340 0.268 0.312
#> TCGA-02-0337-01A-01 4 0.6700 0.04594 0.000 0.416 0.096 0.448 0.040
#> TCGA-06-0122-01A-01 2 0.5968 0.58066 0.000 0.620 0.192 0.180 0.008
#> TCGA-06-0124-01A-01 2 0.4733 0.71102 0.000 0.748 0.092 0.152 0.008
#> TCGA-06-0130-01A-01 2 0.1012 0.75909 0.000 0.968 0.000 0.012 0.020
#> TCGA-06-0139-01A-01 2 0.1386 0.76767 0.000 0.952 0.000 0.032 0.016
#> TCGA-06-0143-01A-01 2 0.5907 0.58892 0.000 0.628 0.188 0.176 0.008
#> TCGA-06-0147-01A-01 2 0.1386 0.76767 0.000 0.952 0.000 0.032 0.016
#> TCGA-06-0149-01A-05 3 0.6751 0.21374 0.000 0.292 0.476 0.224 0.008
#> TCGA-06-0152-01A-02 3 0.6499 0.53431 0.000 0.204 0.616 0.060 0.120
#> TCGA-06-0154-01A-02 2 0.4998 0.69364 0.000 0.724 0.104 0.164 0.008
#> TCGA-06-0164-01A-01 2 0.2532 0.77100 0.000 0.892 0.012 0.088 0.008
#> TCGA-06-0175-01A-01 2 0.6368 0.30983 0.000 0.488 0.180 0.332 0.000
#> TCGA-06-0176-01A-03 2 0.1281 0.75268 0.000 0.956 0.000 0.012 0.032
#> TCGA-06-0184-01A-01 4 0.4774 0.39657 0.000 0.276 0.040 0.680 0.004
#> TCGA-06-0189-01A-05 2 0.1173 0.76847 0.000 0.964 0.004 0.012 0.020
#> TCGA-06-0190-01A-01 2 0.4733 0.71102 0.000 0.748 0.092 0.152 0.008
#> TCGA-06-0194-01A-01 2 0.4932 0.70753 0.000 0.732 0.108 0.152 0.008
#> TCGA-06-0197-01A-02 2 0.1106 0.76558 0.000 0.964 0.000 0.012 0.024
#> TCGA-06-0210-01A-01 2 0.6057 0.57566 0.000 0.608 0.188 0.196 0.008
#> TCGA-06-0397-01A-01 2 0.2761 0.76786 0.000 0.896 0.028 0.048 0.028
#> TCGA-06-0409-01A-02 2 0.2511 0.76915 0.000 0.892 0.016 0.088 0.004
#> TCGA-06-0412-01A-01 2 0.6057 0.57566 0.000 0.608 0.188 0.196 0.008
#> TCGA-06-0644-01A-02 2 0.1300 0.75289 0.000 0.956 0.000 0.016 0.028
#> TCGA-06-0645-01A-01 2 0.4670 0.70602 0.000 0.740 0.064 0.188 0.008
#> TCGA-08-0346-01A-01 2 0.5108 0.69535 0.000 0.716 0.120 0.156 0.008
#> TCGA-08-0352-01A-01 2 0.6719 0.34281 0.000 0.484 0.288 0.220 0.008
#> TCGA-08-0360-01A-01 2 0.3161 0.76482 0.000 0.860 0.044 0.092 0.004
#> TCGA-08-0390-01A-01 4 0.5343 -0.10177 0.000 0.468 0.024 0.492 0.016
#> TCGA-08-0392-01A-01 2 0.1934 0.74037 0.000 0.928 0.004 0.016 0.052
#> TCGA-08-0509-01A-01 2 0.3340 0.73998 0.000 0.824 0.016 0.156 0.004
#> TCGA-08-0510-01A-01 2 0.5510 0.64435 0.000 0.668 0.120 0.204 0.008
#> TCGA-08-0512-01A-01 2 0.2835 0.77230 0.000 0.880 0.036 0.080 0.004
#> TCGA-08-0522-01A-01 2 0.1386 0.75102 0.000 0.952 0.000 0.016 0.032
#> TCGA-12-0619-01A-01 2 0.1485 0.76331 0.000 0.948 0.000 0.020 0.032
#> TCGA-12-0620-01A-01 2 0.6618 0.25223 0.000 0.452 0.372 0.168 0.008
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.6495 0.27672 0.564 0.000 0.164 0.016 0.204 0.052
#> TCGA-02-0010-01A-01 1 0.0000 0.64103 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 5 0.5869 0.34484 0.360 0.000 0.080 0.036 0.520 0.004
#> TCGA-02-0014-01A-01 1 0.0000 0.64103 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0146 0.64031 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0026-01B-01 1 0.5733 0.11677 0.532 0.000 0.116 0.012 0.336 0.004
#> TCGA-02-0028-01A-01 1 0.0000 0.64103 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.6495 0.27672 0.564 0.000 0.164 0.016 0.204 0.052
#> TCGA-02-0047-01A-01 6 0.7277 -0.02990 0.100 0.012 0.136 0.008 0.276 0.468
#> TCGA-02-0048-01A-01 1 0.5137 0.43349 0.680 0.000 0.200 0.008 0.092 0.020
#> TCGA-02-0060-01A-01 5 0.8044 0.45857 0.184 0.000 0.164 0.052 0.412 0.188
#> TCGA-02-0069-01A-01 1 0.0000 0.64103 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.6924 -0.04394 0.464 0.000 0.136 0.016 0.316 0.068
#> TCGA-02-0080-01A-01 5 0.5306 0.20699 0.440 0.000 0.036 0.036 0.488 0.000
#> TCGA-02-0084-01A-03 5 0.5849 0.10948 0.000 0.000 0.096 0.100 0.632 0.172
#> TCGA-02-0087-01A-01 5 0.5849 0.10948 0.000 0.000 0.096 0.100 0.632 0.172
#> TCGA-02-0104-01A-01 1 0.0000 0.64103 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.64103 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.64103 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.7302 -0.27380 0.164 0.000 0.420 0.028 0.320 0.068
#> TCGA-02-0325-01A-01 3 0.7302 -0.27380 0.164 0.000 0.420 0.028 0.320 0.068
#> TCGA-02-0338-01A-01 1 0.0000 0.64103 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.64103 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 5 0.5306 0.20699 0.440 0.000 0.036 0.036 0.488 0.000
#> TCGA-02-0439-01A-01 5 0.7584 0.48842 0.172 0.000 0.116 0.032 0.452 0.228
#> TCGA-02-0440-01A-01 5 0.7491 0.29869 0.336 0.000 0.164 0.016 0.372 0.112
#> TCGA-02-0446-01A-01 6 0.7428 -0.08267 0.112 0.012 0.144 0.008 0.276 0.448
#> TCGA-06-0128-01A-01 5 0.5134 0.11888 0.464 0.000 0.036 0.012 0.480 0.008
#> TCGA-06-0129-01A-01 1 0.4829 -0.06131 0.520 0.000 0.032 0.012 0.436 0.000
#> TCGA-06-0146-01A-01 5 0.5530 0.33834 0.352 0.000 0.060 0.024 0.556 0.008
#> TCGA-06-0156-01A-01 6 0.7317 -0.00397 0.108 0.020 0.128 0.004 0.268 0.472
#> TCGA-06-0166-01A-01 5 0.8024 0.41012 0.220 0.012 0.160 0.008 0.328 0.272
#> TCGA-06-0174-01A-01 1 0.6495 0.27672 0.564 0.000 0.164 0.016 0.204 0.052
#> TCGA-06-0177-01A-01 1 0.6914 -0.22620 0.396 0.000 0.128 0.016 0.396 0.064
#> TCGA-06-0238-01A-02 5 0.7378 0.28145 0.344 0.000 0.132 0.036 0.408 0.080
#> TCGA-06-0241-01A-02 1 0.4353 0.54566 0.756 0.000 0.100 0.004 0.128 0.012
#> TCGA-06-0410-01A-01 1 0.4393 0.54372 0.752 0.000 0.100 0.004 0.132 0.012
#> TCGA-06-0413-01A-01 1 0.0146 0.64031 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-06-0414-01A-01 1 0.6610 0.25447 0.556 0.000 0.132 0.016 0.224 0.072
#> TCGA-06-0646-01A-01 6 0.7317 -0.00397 0.108 0.020 0.128 0.004 0.268 0.472
#> TCGA-06-0648-01A-01 1 0.5746 0.13768 0.536 0.000 0.120 0.012 0.328 0.004
#> TCGA-08-0245-01A-01 1 0.3510 0.58328 0.820 0.000 0.084 0.004 0.088 0.004
#> TCGA-08-0344-01A-01 1 0.2480 0.56998 0.872 0.000 0.024 0.000 0.104 0.000
#> TCGA-08-0347-01A-01 6 0.7428 -0.08267 0.112 0.012 0.144 0.008 0.276 0.448
#> TCGA-08-0348-01A-01 5 0.7735 0.42024 0.248 0.000 0.156 0.016 0.388 0.192
#> TCGA-08-0350-01A-01 5 0.5477 0.31279 0.372 0.000 0.064 0.016 0.540 0.008
#> TCGA-08-0353-01A-01 3 0.5147 0.20345 0.336 0.000 0.592 0.008 0.052 0.012
#> TCGA-08-0359-01A-01 6 0.7130 -0.13991 0.108 0.000 0.140 0.008 0.304 0.440
#> TCGA-08-0385-01A-01 1 0.4202 0.38336 0.712 0.000 0.064 0.000 0.224 0.000
#> TCGA-08-0517-01A-01 1 0.4452 0.54821 0.772 0.000 0.112 0.012 0.072 0.032
#> TCGA-08-0524-01A-01 1 0.0000 0.64103 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.5596 0.26320 0.592 0.000 0.116 0.004 0.272 0.016
#> TCGA-12-0618-01A-01 1 0.5746 0.13768 0.536 0.000 0.120 0.012 0.328 0.004
#> TCGA-02-0089-01A-01 6 0.4898 0.47695 0.000 0.180 0.076 0.012 0.020 0.712
#> TCGA-02-0113-01A-01 3 0.5883 0.54236 0.000 0.012 0.620 0.052 0.088 0.228
#> TCGA-02-0115-01A-01 6 0.2271 0.44197 0.000 0.036 0.000 0.032 0.024 0.908
#> TCGA-02-0451-01A-01 6 0.4423 0.51124 0.000 0.112 0.068 0.020 0.024 0.776
#> TCGA-06-0132-01A-02 6 0.2351 0.44060 0.000 0.036 0.000 0.032 0.028 0.904
#> TCGA-06-0133-01A-02 6 0.5949 0.12368 0.000 0.000 0.052 0.196 0.152 0.600
#> TCGA-06-0138-01A-02 6 0.5878 0.38967 0.016 0.036 0.048 0.084 0.124 0.692
#> TCGA-06-0160-01A-01 4 0.4392 1.00000 0.000 0.000 0.000 0.720 0.136 0.144
#> TCGA-06-0162-01A-01 6 0.4857 0.18032 0.000 0.008 0.000 0.196 0.116 0.680
#> TCGA-06-0167-01A-01 4 0.4392 1.00000 0.000 0.000 0.000 0.720 0.136 0.144
#> TCGA-06-0171-01A-02 6 0.5849 0.38674 0.016 0.032 0.048 0.084 0.128 0.692
#> TCGA-06-0173-01A-01 6 0.5526 0.42855 0.004 0.208 0.100 0.004 0.032 0.652
#> TCGA-06-0179-01A-02 6 0.2351 0.44060 0.000 0.036 0.000 0.032 0.028 0.904
#> TCGA-06-0182-01A-01 3 0.6632 0.12782 0.000 0.008 0.432 0.072 0.100 0.388
#> TCGA-06-0185-01A-01 3 0.6694 0.31787 0.000 0.012 0.492 0.088 0.092 0.316
#> TCGA-06-0195-01B-01 6 0.6366 -0.05115 0.008 0.000 0.032 0.256 0.176 0.528
#> TCGA-06-0208-01B-01 6 0.6081 0.11788 0.000 0.000 0.064 0.192 0.152 0.592
#> TCGA-06-0214-01A-02 6 0.4770 0.51120 0.004 0.104 0.064 0.020 0.044 0.764
#> TCGA-06-0219-01A-01 6 0.5980 0.02557 0.000 0.000 0.036 0.244 0.152 0.568
#> TCGA-06-0221-01A-01 6 0.6739 -0.09175 0.028 0.000 0.032 0.248 0.180 0.512
#> TCGA-06-0237-01A-02 6 0.6073 0.14897 0.000 0.000 0.068 0.188 0.148 0.596
#> TCGA-06-0240-01A-02 4 0.4392 1.00000 0.000 0.000 0.000 0.720 0.136 0.144
#> TCGA-08-0349-01A-01 6 0.6104 0.34391 0.000 0.016 0.136 0.100 0.108 0.640
#> TCGA-08-0380-01A-01 6 0.2541 0.45591 0.000 0.052 0.000 0.024 0.032 0.892
#> TCGA-08-0386-01A-01 3 0.6423 0.51218 0.028 0.000 0.592 0.052 0.132 0.196
#> TCGA-08-0520-01A-01 3 0.6353 0.35325 0.000 0.000 0.500 0.052 0.140 0.308
#> TCGA-02-0007-01A-01 3 0.5027 0.62993 0.032 0.000 0.740 0.064 0.120 0.044
#> TCGA-02-0009-01A-01 3 0.0665 0.74568 0.000 0.000 0.980 0.004 0.008 0.008
#> TCGA-02-0016-01A-01 3 0.1622 0.74271 0.000 0.000 0.940 0.016 0.028 0.016
#> TCGA-02-0021-01A-01 3 0.0665 0.74600 0.000 0.000 0.980 0.008 0.004 0.008
#> TCGA-02-0023-01B-01 3 0.5835 0.56687 0.000 0.124 0.640 0.028 0.024 0.184
#> TCGA-02-0027-01A-01 5 0.7966 0.39775 0.112 0.000 0.312 0.044 0.344 0.188
#> TCGA-02-0038-01A-01 6 0.5626 0.41682 0.000 0.192 0.140 0.008 0.024 0.636
#> TCGA-02-0043-01A-01 3 0.0508 0.74495 0.004 0.000 0.984 0.012 0.000 0.000
#> TCGA-02-0070-01A-01 2 0.6403 0.45862 0.000 0.500 0.232 0.012 0.016 0.240
#> TCGA-02-0102-01A-01 3 0.1266 0.74939 0.004 0.008 0.960 0.016 0.004 0.008
#> TCGA-02-0260-01A-03 3 0.2747 0.70959 0.004 0.000 0.868 0.028 0.096 0.004
#> TCGA-02-0269-01B-01 3 0.2747 0.70959 0.004 0.000 0.868 0.028 0.096 0.004
#> TCGA-02-0285-01A-01 3 0.1980 0.74680 0.000 0.016 0.920 0.000 0.016 0.048
#> TCGA-02-0289-01A-01 3 0.1257 0.74052 0.000 0.000 0.952 0.020 0.028 0.000
#> TCGA-02-0290-01A-01 3 0.2936 0.74157 0.000 0.044 0.880 0.020 0.036 0.020
#> TCGA-02-0317-01A-01 3 0.3646 0.68051 0.008 0.000 0.804 0.048 0.136 0.004
#> TCGA-02-0333-01A-02 3 0.2747 0.70959 0.004 0.000 0.868 0.028 0.096 0.004
#> TCGA-02-0422-01A-01 3 0.3911 0.69724 0.004 0.032 0.796 0.004 0.024 0.140
#> TCGA-02-0430-01A-01 3 0.1980 0.74680 0.000 0.016 0.920 0.000 0.016 0.048
#> TCGA-06-0125-01A-01 3 0.0665 0.74524 0.000 0.000 0.980 0.008 0.008 0.004
#> TCGA-06-0126-01A-01 3 0.0912 0.74549 0.004 0.000 0.972 0.004 0.012 0.008
#> TCGA-06-0137-01A-03 3 0.1262 0.74588 0.000 0.000 0.956 0.020 0.016 0.008
#> TCGA-06-0145-01A-04 3 0.2899 0.72827 0.000 0.016 0.860 0.004 0.016 0.104
#> TCGA-06-0148-01A-01 3 0.2726 0.74375 0.000 0.032 0.892 0.028 0.032 0.016
#> TCGA-06-0187-01A-01 3 0.4639 0.63455 0.000 0.068 0.728 0.004 0.024 0.176
#> TCGA-06-0211-01B-01 3 0.1377 0.74821 0.004 0.000 0.952 0.004 0.024 0.016
#> TCGA-06-0402-01A-01 3 0.0405 0.74487 0.004 0.000 0.988 0.008 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.6013 0.43375 0.000 0.152 0.564 0.016 0.012 0.256
#> TCGA-08-0354-01A-01 3 0.5523 0.56994 0.000 0.160 0.664 0.012 0.028 0.136
#> TCGA-08-0355-01A-01 3 0.6111 0.46220 0.000 0.168 0.576 0.020 0.016 0.220
#> TCGA-08-0357-01A-01 3 0.3911 0.69724 0.004 0.032 0.796 0.004 0.024 0.140
#> TCGA-08-0358-01A-01 3 0.3646 0.68051 0.008 0.000 0.804 0.048 0.136 0.004
#> TCGA-08-0375-01A-01 3 0.3001 0.70322 0.008 0.000 0.852 0.028 0.108 0.004
#> TCGA-08-0511-01A-01 3 0.4778 0.63803 0.000 0.068 0.728 0.012 0.024 0.168
#> TCGA-08-0514-01A-01 3 0.4767 0.63077 0.000 0.072 0.724 0.008 0.024 0.172
#> TCGA-08-0518-01A-01 3 0.1317 0.75097 0.000 0.016 0.956 0.016 0.008 0.004
#> TCGA-08-0529-01A-02 3 0.1980 0.74680 0.000 0.016 0.920 0.000 0.016 0.048
#> TCGA-08-0531-01A-01 3 0.0924 0.75046 0.000 0.004 0.972 0.008 0.008 0.008
#> TCGA-02-0057-01A-01 6 0.4638 0.47114 0.000 0.176 0.072 0.008 0.016 0.728
#> TCGA-02-0004-01A-01 2 0.1464 0.70959 0.000 0.944 0.000 0.036 0.016 0.004
#> TCGA-02-0006-01B-01 6 0.5258 0.38146 0.000 0.232 0.092 0.008 0.016 0.652
#> TCGA-02-0025-01A-01 2 0.3438 0.63956 0.000 0.828 0.008 0.100 0.060 0.004
#> TCGA-02-0033-01A-01 2 0.1434 0.72302 0.000 0.948 0.000 0.024 0.008 0.020
#> TCGA-02-0034-01A-01 2 0.3765 0.72931 0.000 0.812 0.036 0.012 0.020 0.120
#> TCGA-02-0039-01A-01 2 0.5189 0.47207 0.000 0.564 0.036 0.012 0.016 0.372
#> TCGA-02-0051-01A-01 2 0.3678 0.61856 0.000 0.788 0.000 0.128 0.084 0.000
#> TCGA-02-0054-01A-01 6 0.5301 0.17474 0.000 0.324 0.084 0.004 0.008 0.580
#> TCGA-02-0055-01A-01 2 0.1536 0.70777 0.000 0.940 0.000 0.040 0.016 0.004
#> TCGA-02-0059-01A-01 2 0.1426 0.71673 0.000 0.948 0.000 0.028 0.016 0.008
#> TCGA-02-0064-01A-01 2 0.3672 0.70935 0.000 0.780 0.036 0.000 0.008 0.176
#> TCGA-02-0075-01A-01 2 0.4845 0.67688 0.000 0.700 0.072 0.008 0.016 0.204
#> TCGA-02-0079-01A-03 6 0.7811 0.12127 0.000 0.328 0.076 0.108 0.100 0.388
#> TCGA-02-0085-01A-01 6 0.5461 0.20857 0.000 0.316 0.056 0.012 0.024 0.592
#> TCGA-02-0086-01A-01 2 0.4795 0.70535 0.000 0.736 0.064 0.024 0.020 0.156
#> TCGA-02-0099-01A-01 6 0.5034 -0.07939 0.000 0.404 0.056 0.000 0.008 0.532
#> TCGA-02-0106-01A-01 2 0.2734 0.68430 0.000 0.876 0.004 0.064 0.052 0.004
#> TCGA-02-0107-01A-01 2 0.2113 0.73145 0.000 0.896 0.008 0.004 0.000 0.092
#> TCGA-02-0111-01A-01 2 0.2325 0.73216 0.000 0.884 0.008 0.008 0.000 0.100
#> TCGA-02-0326-01A-01 3 0.8405 -0.17088 0.004 0.036 0.284 0.212 0.232 0.232
#> TCGA-02-0337-01A-01 6 0.5938 0.13489 0.000 0.348 0.064 0.004 0.056 0.528
#> TCGA-06-0122-01A-01 2 0.6124 0.52850 0.000 0.548 0.168 0.012 0.016 0.256
#> TCGA-06-0124-01A-01 2 0.5120 0.65770 0.000 0.672 0.076 0.012 0.016 0.224
#> TCGA-06-0130-01A-01 2 0.1296 0.71282 0.000 0.952 0.000 0.032 0.012 0.004
#> TCGA-06-0139-01A-01 2 0.1340 0.72637 0.000 0.948 0.000 0.008 0.004 0.040
#> TCGA-06-0143-01A-01 2 0.6080 0.53640 0.000 0.556 0.164 0.012 0.016 0.252
#> TCGA-06-0147-01A-01 2 0.1340 0.72637 0.000 0.948 0.000 0.008 0.004 0.040
#> TCGA-06-0149-01A-05 3 0.6580 0.18906 0.000 0.244 0.444 0.020 0.008 0.284
#> TCGA-06-0152-01A-02 3 0.6978 0.53891 0.000 0.136 0.580 0.100 0.116 0.068
#> TCGA-06-0154-01A-02 2 0.5237 0.63891 0.000 0.652 0.088 0.008 0.016 0.236
#> TCGA-06-0164-01A-01 2 0.2754 0.73152 0.000 0.860 0.012 0.008 0.004 0.116
#> TCGA-06-0175-01A-01 2 0.6457 0.20207 0.000 0.408 0.148 0.012 0.024 0.408
#> TCGA-06-0176-01A-03 2 0.2197 0.69282 0.000 0.900 0.000 0.056 0.044 0.000
#> TCGA-06-0184-01A-01 6 0.4097 0.44231 0.000 0.208 0.032 0.008 0.008 0.744
#> TCGA-06-0189-01A-05 2 0.1854 0.72288 0.000 0.932 0.004 0.028 0.016 0.020
#> TCGA-06-0190-01A-01 2 0.5120 0.65770 0.000 0.672 0.076 0.012 0.016 0.224
#> TCGA-06-0194-01A-01 2 0.5297 0.65194 0.000 0.652 0.100 0.008 0.016 0.224
#> TCGA-06-0197-01A-02 2 0.1346 0.72173 0.000 0.952 0.000 0.024 0.008 0.016
#> TCGA-06-0210-01A-01 2 0.6162 0.52379 0.000 0.536 0.164 0.012 0.016 0.272
#> TCGA-06-0397-01A-01 2 0.4283 0.69561 0.000 0.796 0.024 0.088 0.052 0.040
#> TCGA-06-0409-01A-02 2 0.2846 0.72709 0.000 0.840 0.016 0.004 0.000 0.140
#> TCGA-06-0412-01A-01 2 0.6162 0.52379 0.000 0.536 0.164 0.012 0.016 0.272
#> TCGA-06-0644-01A-02 2 0.2499 0.68318 0.000 0.880 0.000 0.072 0.048 0.000
#> TCGA-06-0645-01A-01 2 0.4793 0.64594 0.000 0.664 0.048 0.004 0.016 0.268
#> TCGA-08-0346-01A-01 2 0.5441 0.63886 0.000 0.636 0.112 0.008 0.016 0.228
#> TCGA-08-0352-01A-01 2 0.6675 0.30596 0.000 0.412 0.260 0.012 0.016 0.300
#> TCGA-08-0360-01A-01 2 0.3770 0.71754 0.000 0.788 0.036 0.000 0.020 0.156
#> TCGA-08-0390-01A-01 6 0.5074 -0.03334 0.000 0.412 0.020 0.012 0.020 0.536
#> TCGA-08-0392-01A-01 2 0.3678 0.61856 0.000 0.788 0.000 0.128 0.084 0.000
#> TCGA-08-0509-01A-01 2 0.3430 0.69974 0.000 0.772 0.016 0.004 0.000 0.208
#> TCGA-08-0510-01A-01 2 0.5655 0.58525 0.000 0.596 0.100 0.012 0.016 0.276
#> TCGA-08-0512-01A-01 2 0.3319 0.73069 0.000 0.828 0.028 0.012 0.004 0.128
#> TCGA-08-0522-01A-01 2 0.2724 0.67678 0.000 0.864 0.000 0.084 0.052 0.000
#> TCGA-12-0619-01A-01 2 0.2016 0.71326 0.000 0.920 0.000 0.040 0.024 0.016
#> TCGA-12-0620-01A-01 2 0.6849 0.20541 0.000 0.388 0.344 0.016 0.024 0.228
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> MAD:hclust 148 5.03e-30 2
#> MAD:hclust 107 1.66e-42 3
#> MAD:hclust 124 1.99e-66 4
#> MAD:hclust 99 1.58e-48 5
#> MAD:hclust 98 4.59e-48 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "kmeans"]
# you can also extract it by
# res = res_list["MAD:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.785 0.878 0.949 0.4958 0.499 0.499
#> 3 3 0.835 0.874 0.945 0.3333 0.671 0.435
#> 4 4 0.967 0.942 0.972 0.1346 0.864 0.624
#> 5 5 0.769 0.681 0.807 0.0516 0.986 0.944
#> 6 6 0.735 0.624 0.779 0.0350 0.924 0.696
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.9954 0.1273 0.540 0.460
#> TCGA-02-0048-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0084-01A-03 2 0.8608 0.6155 0.284 0.716
#> TCGA-02-0087-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0104-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.0938 0.9378 0.988 0.012
#> TCGA-02-0325-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0446-01A-01 2 0.9998 0.0444 0.492 0.508
#> TCGA-06-0128-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.6531 0.7801 0.832 0.168
#> TCGA-06-0166-01A-01 1 0.6343 0.7888 0.840 0.160
#> TCGA-06-0174-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.8207 0.6676 0.256 0.744
#> TCGA-06-0648-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.4298 0.8711 0.912 0.088
#> TCGA-08-0348-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-08-0353-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.4939 0.8559 0.108 0.892
#> TCGA-02-0115-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.6438 0.7933 0.164 0.836
#> TCGA-06-0138-01A-02 2 0.8207 0.6672 0.256 0.744
#> TCGA-06-0160-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0171-01A-02 1 0.9896 0.1980 0.560 0.440
#> TCGA-06-0173-01A-01 2 0.8081 0.6800 0.248 0.752
#> TCGA-06-0179-01A-02 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.8267 0.6606 0.260 0.740
#> TCGA-06-0185-01A-01 2 0.9358 0.4809 0.352 0.648
#> TCGA-06-0195-01B-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.9209 0.5175 0.336 0.664
#> TCGA-06-0214-01A-02 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0219-01A-01 1 0.9896 0.1963 0.560 0.440
#> TCGA-06-0221-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-06-0237-01A-02 1 0.2236 0.9195 0.964 0.036
#> TCGA-06-0240-01A-02 1 0.0938 0.9367 0.988 0.012
#> TCGA-08-0349-01A-01 1 0.9393 0.4403 0.644 0.356
#> TCGA-08-0380-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.0938 0.9378 0.988 0.012
#> TCGA-08-0520-01A-01 2 0.7950 0.6938 0.240 0.760
#> TCGA-02-0007-01A-01 1 0.0938 0.9378 0.988 0.012
#> TCGA-02-0009-01A-01 1 0.2043 0.9229 0.968 0.032
#> TCGA-02-0016-01A-01 1 0.0938 0.9378 0.988 0.012
#> TCGA-02-0021-01A-01 1 0.9710 0.3261 0.600 0.400
#> TCGA-02-0023-01B-01 2 0.3584 0.8931 0.068 0.932
#> TCGA-02-0027-01A-01 1 0.6623 0.7738 0.828 0.172
#> TCGA-02-0038-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0043-01A-01 1 0.5737 0.8179 0.864 0.136
#> TCGA-02-0070-01A-01 2 0.1633 0.9291 0.024 0.976
#> TCGA-02-0102-01A-01 1 0.9909 0.1859 0.556 0.444
#> TCGA-02-0260-01A-03 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0269-01B-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-02-0285-01A-01 2 0.1184 0.9347 0.016 0.984
#> TCGA-02-0289-01A-01 1 0.0938 0.9378 0.988 0.012
#> TCGA-02-0290-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0317-01A-01 1 0.0938 0.9378 0.988 0.012
#> TCGA-02-0333-01A-02 1 0.0938 0.9378 0.988 0.012
#> TCGA-02-0422-01A-01 2 0.9000 0.5580 0.316 0.684
#> TCGA-02-0430-01A-01 1 0.9552 0.3906 0.624 0.376
#> TCGA-06-0125-01A-01 1 0.0938 0.9378 0.988 0.012
#> TCGA-06-0126-01A-01 1 0.0672 0.9398 0.992 0.008
#> TCGA-06-0137-01A-03 1 0.0938 0.9378 0.988 0.012
#> TCGA-06-0145-01A-04 2 0.1184 0.9347 0.016 0.984
#> TCGA-06-0148-01A-01 2 0.2043 0.9232 0.032 0.968
#> TCGA-06-0187-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0211-01B-01 1 0.0938 0.9378 0.988 0.012
#> TCGA-06-0402-01A-01 2 0.9635 0.3939 0.388 0.612
#> TCGA-08-0246-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.1184 0.9347 0.016 0.984
#> TCGA-08-0357-01A-01 1 0.8661 0.5870 0.712 0.288
#> TCGA-08-0358-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-08-0375-01A-01 1 0.0000 0.9434 1.000 0.000
#> TCGA-08-0511-01A-01 2 0.1184 0.9347 0.016 0.984
#> TCGA-08-0514-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.4939 0.8556 0.108 0.892
#> TCGA-08-0529-01A-02 2 0.7883 0.6982 0.236 0.764
#> TCGA-08-0531-01A-01 2 0.9170 0.5248 0.332 0.668
#> TCGA-02-0057-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-02-0326-01A-01 1 0.0938 0.9378 0.988 0.012
#> TCGA-02-0337-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.2236 0.9200 0.036 0.964
#> TCGA-06-0154-01A-02 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9448 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9448 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.9448 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 3 0.6079 0.3544 0.388 0.000 0.612
#> TCGA-02-0048-01A-01 1 0.4842 0.7186 0.776 0.000 0.224
#> TCGA-02-0060-01A-01 1 0.4654 0.7530 0.792 0.000 0.208
#> TCGA-02-0069-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0084-01A-03 3 0.7504 0.5134 0.060 0.312 0.628
#> TCGA-02-0087-01A-01 1 0.4654 0.7530 0.792 0.000 0.208
#> TCGA-02-0104-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.1964 0.8783 0.056 0.000 0.944
#> TCGA-02-0325-01A-01 1 0.0237 0.9450 0.996 0.000 0.004
#> TCGA-02-0338-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0439-01A-01 3 0.5678 0.5241 0.316 0.000 0.684
#> TCGA-02-0440-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.7378 0.2856 0.560 0.036 0.404
#> TCGA-06-0128-01A-01 1 0.0747 0.9379 0.984 0.000 0.016
#> TCGA-06-0129-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 3 0.6298 0.3496 0.388 0.004 0.608
#> TCGA-06-0166-01A-01 3 0.6168 0.2862 0.412 0.000 0.588
#> TCGA-06-0174-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.0592 0.9401 0.988 0.000 0.012
#> TCGA-06-0241-01A-02 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0237 0.9449 0.996 0.000 0.004
#> TCGA-06-0413-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.3644 0.8159 0.004 0.124 0.872
#> TCGA-06-0648-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-08-0347-01A-01 3 0.5621 0.5395 0.308 0.000 0.692
#> TCGA-08-0348-01A-01 1 0.0237 0.9451 0.996 0.000 0.004
#> TCGA-08-0350-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-08-0353-01A-01 3 0.0892 0.9029 0.020 0.000 0.980
#> TCGA-08-0359-01A-01 1 0.4702 0.7486 0.788 0.000 0.212
#> TCGA-08-0385-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.9475 1.000 0.000 0.000
#> TCGA-02-0089-01A-01 3 0.6180 0.3383 0.000 0.416 0.584
#> TCGA-02-0113-01A-01 3 0.0000 0.9064 0.000 0.000 1.000
#> TCGA-02-0115-01A-01 3 0.5926 0.4775 0.000 0.356 0.644
#> TCGA-02-0451-01A-01 3 0.6180 0.3383 0.000 0.416 0.584
#> TCGA-06-0132-01A-02 2 0.4842 0.6842 0.000 0.776 0.224
#> TCGA-06-0133-01A-02 3 0.0000 0.9064 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 3 0.1163 0.8929 0.000 0.028 0.972
#> TCGA-06-0160-01A-01 1 0.4750 0.7472 0.784 0.000 0.216
#> TCGA-06-0162-01A-01 3 0.5948 0.4686 0.000 0.360 0.640
#> TCGA-06-0167-01A-01 1 0.4750 0.7472 0.784 0.000 0.216
#> TCGA-06-0171-01A-02 3 0.0424 0.9046 0.008 0.000 0.992
#> TCGA-06-0173-01A-01 3 0.0237 0.9061 0.000 0.004 0.996
#> TCGA-06-0179-01A-02 2 0.5098 0.6409 0.000 0.752 0.248
#> TCGA-06-0182-01A-01 3 0.0000 0.9064 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 3 0.0000 0.9064 0.000 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.4750 0.7472 0.784 0.000 0.216
#> TCGA-06-0208-01B-01 3 0.0000 0.9064 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 3 0.5098 0.6633 0.000 0.248 0.752
#> TCGA-06-0219-01A-01 3 0.0424 0.9046 0.008 0.000 0.992
#> TCGA-06-0221-01A-01 1 0.3412 0.8495 0.876 0.000 0.124
#> TCGA-06-0237-01A-02 3 0.0000 0.9064 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 1 0.4750 0.7472 0.784 0.000 0.216
#> TCGA-08-0349-01A-01 3 0.0000 0.9064 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 3 0.6309 0.0838 0.000 0.496 0.504
#> TCGA-08-0386-01A-01 3 0.0237 0.9070 0.004 0.000 0.996
#> TCGA-08-0520-01A-01 3 0.0000 0.9064 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.0592 0.9068 0.012 0.000 0.988
#> TCGA-02-0009-01A-01 3 0.0592 0.9068 0.012 0.000 0.988
#> TCGA-02-0016-01A-01 3 0.0424 0.9074 0.008 0.000 0.992
#> TCGA-02-0021-01A-01 3 0.0592 0.9068 0.012 0.000 0.988
#> TCGA-02-0023-01B-01 3 0.0237 0.9070 0.000 0.004 0.996
#> TCGA-02-0027-01A-01 3 0.0424 0.9074 0.008 0.000 0.992
#> TCGA-02-0038-01A-01 3 0.0000 0.9064 0.000 0.000 1.000
#> TCGA-02-0043-01A-01 3 0.2796 0.8382 0.092 0.000 0.908
#> TCGA-02-0070-01A-01 3 0.0592 0.9060 0.000 0.012 0.988
#> TCGA-02-0102-01A-01 3 0.0592 0.9068 0.012 0.000 0.988
#> TCGA-02-0260-01A-03 3 0.4062 0.7543 0.164 0.000 0.836
#> TCGA-02-0269-01B-01 3 0.0747 0.9052 0.016 0.000 0.984
#> TCGA-02-0285-01A-01 3 0.0592 0.9060 0.000 0.012 0.988
#> TCGA-02-0289-01A-01 3 0.0592 0.9068 0.012 0.000 0.988
#> TCGA-02-0290-01A-01 3 0.0592 0.9060 0.000 0.012 0.988
#> TCGA-02-0317-01A-01 3 0.0747 0.9052 0.016 0.000 0.984
#> TCGA-02-0333-01A-02 3 0.0747 0.9052 0.016 0.000 0.984
#> TCGA-02-0422-01A-01 3 0.0424 0.9074 0.008 0.000 0.992
#> TCGA-02-0430-01A-01 3 0.0592 0.9068 0.012 0.000 0.988
#> TCGA-06-0125-01A-01 3 0.0747 0.9052 0.016 0.000 0.984
#> TCGA-06-0126-01A-01 3 0.0592 0.9068 0.012 0.000 0.988
#> TCGA-06-0137-01A-03 3 0.0424 0.9074 0.008 0.000 0.992
#> TCGA-06-0145-01A-04 3 0.0424 0.9069 0.000 0.008 0.992
#> TCGA-06-0148-01A-01 3 0.0747 0.9043 0.000 0.016 0.984
#> TCGA-06-0187-01A-01 3 0.0592 0.9060 0.000 0.012 0.988
#> TCGA-06-0211-01B-01 3 0.0592 0.9068 0.012 0.000 0.988
#> TCGA-06-0402-01A-01 3 0.0661 0.9074 0.008 0.004 0.988
#> TCGA-08-0246-01A-01 3 0.0592 0.9060 0.000 0.012 0.988
#> TCGA-08-0354-01A-01 3 0.0592 0.9060 0.000 0.012 0.988
#> TCGA-08-0355-01A-01 3 0.0237 0.9070 0.000 0.004 0.996
#> TCGA-08-0357-01A-01 3 0.0424 0.9074 0.008 0.000 0.992
#> TCGA-08-0358-01A-01 3 0.0747 0.9052 0.016 0.000 0.984
#> TCGA-08-0375-01A-01 3 0.0747 0.9052 0.016 0.000 0.984
#> TCGA-08-0511-01A-01 3 0.0424 0.9069 0.000 0.008 0.992
#> TCGA-08-0514-01A-01 3 0.0592 0.9060 0.000 0.012 0.988
#> TCGA-08-0518-01A-01 3 0.0661 0.9071 0.004 0.008 0.988
#> TCGA-08-0529-01A-02 3 0.0475 0.9077 0.004 0.004 0.992
#> TCGA-08-0531-01A-01 3 0.0424 0.9074 0.008 0.000 0.992
#> TCGA-02-0057-01A-01 3 0.6192 0.3330 0.000 0.420 0.580
#> TCGA-02-0004-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.0237 0.9697 0.000 0.996 0.004
#> TCGA-02-0025-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0054-01A-01 2 0.0592 0.9629 0.000 0.988 0.012
#> TCGA-02-0055-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0079-01A-03 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0085-01A-01 2 0.0747 0.9604 0.000 0.984 0.016
#> TCGA-02-0086-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0099-01A-01 2 0.0424 0.9663 0.000 0.992 0.008
#> TCGA-02-0106-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-02-0326-01A-01 3 0.0592 0.9066 0.012 0.000 0.988
#> TCGA-02-0337-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0122-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0124-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0143-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 2 0.4654 0.7115 0.000 0.792 0.208
#> TCGA-06-0152-01A-02 3 0.0592 0.9060 0.000 0.012 0.988
#> TCGA-06-0154-01A-02 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 2 0.6286 0.0226 0.000 0.536 0.464
#> TCGA-06-0176-01A-03 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0412-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-08-0352-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-08-0392-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9729 0.000 1.000 0.000
#> TCGA-12-0620-01A-01 2 0.3412 0.8394 0.000 0.876 0.124
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.2081 0.9031 0.916 0.000 0.000 0.084
#> TCGA-02-0010-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0336 0.9824 0.992 0.000 0.000 0.008
#> TCGA-02-0014-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-02-0048-01A-01 1 0.0336 0.9802 0.992 0.000 0.008 0.000
#> TCGA-02-0060-01A-01 4 0.1637 0.9092 0.060 0.000 0.000 0.940
#> TCGA-02-0069-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.0336 0.9824 0.992 0.000 0.000 0.008
#> TCGA-02-0084-01A-03 4 0.3726 0.7134 0.000 0.000 0.212 0.788
#> TCGA-02-0087-01A-01 4 0.4534 0.7851 0.068 0.000 0.132 0.800
#> TCGA-02-0104-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.2530 0.8760 0.004 0.000 0.896 0.100
#> TCGA-02-0325-01A-01 1 0.4086 0.7205 0.776 0.000 0.216 0.008
#> TCGA-02-0338-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0336 0.9824 0.992 0.000 0.000 0.008
#> TCGA-02-0439-01A-01 4 0.0000 0.9479 0.000 0.000 0.000 1.000
#> TCGA-02-0440-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0128-01A-01 4 0.1940 0.8947 0.076 0.000 0.000 0.924
#> TCGA-06-0129-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0336 0.9824 0.992 0.000 0.000 0.008
#> TCGA-06-0156-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0166-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0174-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-06-0238-01A-02 4 0.4522 0.5289 0.320 0.000 0.000 0.680
#> TCGA-06-0241-01A-02 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0648-01A-01 1 0.0188 0.9845 0.996 0.000 0.000 0.004
#> TCGA-08-0245-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-08-0348-01A-01 1 0.2704 0.8562 0.876 0.000 0.000 0.124
#> TCGA-08-0350-01A-01 1 0.0336 0.9824 0.992 0.000 0.000 0.008
#> TCGA-08-0353-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-08-0359-01A-01 4 0.0000 0.9479 0.000 0.000 0.000 1.000
#> TCGA-08-0385-01A-01 1 0.0188 0.9845 0.996 0.000 0.000 0.004
#> TCGA-08-0517-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.9864 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-02-0113-01A-01 3 0.4500 0.5581 0.000 0.000 0.684 0.316
#> TCGA-02-0115-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-02-0451-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0132-01A-02 4 0.0376 0.9494 0.000 0.004 0.004 0.992
#> TCGA-06-0133-01A-02 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0138-01A-02 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0160-01A-01 4 0.1557 0.9125 0.056 0.000 0.000 0.944
#> TCGA-06-0162-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0167-01A-01 4 0.1557 0.9125 0.056 0.000 0.000 0.944
#> TCGA-06-0171-01A-02 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0173-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0179-01A-02 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0182-01A-01 3 0.4500 0.5578 0.000 0.000 0.684 0.316
#> TCGA-06-0185-01A-01 3 0.4522 0.5500 0.000 0.000 0.680 0.320
#> TCGA-06-0195-01B-01 4 0.0927 0.9437 0.016 0.000 0.008 0.976
#> TCGA-06-0208-01B-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0214-01A-02 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0219-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0221-01A-01 4 0.1557 0.9125 0.056 0.000 0.000 0.944
#> TCGA-06-0237-01A-02 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-06-0240-01A-02 4 0.0000 0.9479 0.000 0.000 0.000 1.000
#> TCGA-08-0349-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-08-0380-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-08-0386-01A-01 3 0.4564 0.5371 0.000 0.000 0.672 0.328
#> TCGA-08-0520-01A-01 4 0.2345 0.8681 0.000 0.000 0.100 0.900
#> TCGA-02-0007-01A-01 3 0.3024 0.8156 0.000 0.000 0.852 0.148
#> TCGA-02-0009-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-02-0016-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-02-0021-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-02-0027-01A-01 3 0.0592 0.9494 0.000 0.000 0.984 0.016
#> TCGA-02-0038-01A-01 4 0.4998 -0.0308 0.000 0.000 0.488 0.512
#> TCGA-02-0043-01A-01 3 0.0188 0.9585 0.004 0.000 0.996 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-02-0260-01A-03 3 0.0336 0.9564 0.000 0.000 0.992 0.008
#> TCGA-02-0269-01B-01 3 0.0336 0.9564 0.000 0.000 0.992 0.008
#> TCGA-02-0285-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-02-0317-01A-01 3 0.0336 0.9564 0.000 0.000 0.992 0.008
#> TCGA-02-0333-01A-02 3 0.0336 0.9564 0.000 0.000 0.992 0.008
#> TCGA-02-0422-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-06-0137-01A-03 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-08-0354-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-08-0357-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-08-0358-01A-01 3 0.0336 0.9564 0.000 0.000 0.992 0.008
#> TCGA-08-0375-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.9613 0.000 0.000 1.000 0.000
#> TCGA-02-0057-01A-01 4 0.0336 0.9519 0.000 0.000 0.008 0.992
#> TCGA-02-0004-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.2888 0.8723 0.000 0.872 0.004 0.124
#> TCGA-02-0025-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0921 0.9677 0.000 0.972 0.000 0.028
#> TCGA-02-0051-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.2976 0.8716 0.000 0.872 0.008 0.120
#> TCGA-02-0055-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0079-01A-03 2 0.0188 0.9828 0.000 0.996 0.000 0.004
#> TCGA-02-0085-01A-01 4 0.0336 0.9466 0.000 0.008 0.000 0.992
#> TCGA-02-0086-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.2918 0.8757 0.000 0.876 0.008 0.116
#> TCGA-02-0106-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0336 0.9564 0.000 0.000 0.992 0.008
#> TCGA-02-0337-01A-01 2 0.1637 0.9433 0.000 0.940 0.000 0.060
#> TCGA-06-0122-01A-01 2 0.1022 0.9607 0.000 0.968 0.032 0.000
#> TCGA-06-0124-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 2 0.1022 0.9607 0.000 0.968 0.032 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.1398 0.9563 0.000 0.956 0.004 0.040
#> TCGA-06-0152-01A-02 3 0.0336 0.9564 0.000 0.000 0.992 0.008
#> TCGA-06-0154-01A-02 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.1890 0.9401 0.000 0.936 0.008 0.056
#> TCGA-06-0176-01A-03 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.1557 0.9464 0.000 0.944 0.000 0.056
#> TCGA-06-0189-01A-05 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.0188 0.9823 0.000 0.996 0.004 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-08-0352-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.0921 0.9679 0.000 0.972 0.000 0.028
#> TCGA-08-0392-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9850 0.000 1.000 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.1389 0.9471 0.000 0.952 0.048 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.3840 0.7636 0.808 0.000 0.000 0.076 0.116
#> TCGA-02-0010-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.4182 0.4624 0.600 0.000 0.000 0.000 0.400
#> TCGA-02-0014-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.2677 0.8363 0.872 0.000 0.000 0.016 0.112
#> TCGA-02-0047-01A-01 4 0.2723 0.6121 0.000 0.000 0.012 0.864 0.124
#> TCGA-02-0048-01A-01 1 0.2943 0.8287 0.880 0.000 0.052 0.008 0.060
#> TCGA-02-0060-01A-01 5 0.5509 0.4546 0.064 0.000 0.000 0.464 0.472
#> TCGA-02-0069-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.2230 0.8448 0.884 0.000 0.000 0.000 0.116
#> TCGA-02-0080-01A-01 1 0.4262 0.3364 0.560 0.000 0.000 0.000 0.440
#> TCGA-02-0084-01A-03 5 0.5999 0.4424 0.000 0.076 0.016 0.376 0.532
#> TCGA-02-0087-01A-01 5 0.5498 0.4947 0.020 0.012 0.012 0.428 0.528
#> TCGA-02-0104-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.6873 0.1234 0.004 0.000 0.412 0.300 0.284
#> TCGA-02-0325-01A-01 5 0.5905 -0.2066 0.420 0.000 0.088 0.004 0.488
#> TCGA-02-0338-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.4262 0.3364 0.560 0.000 0.000 0.000 0.440
#> TCGA-02-0439-01A-01 4 0.4641 -0.3929 0.000 0.000 0.012 0.532 0.456
#> TCGA-02-0440-01A-01 1 0.2338 0.8442 0.884 0.000 0.000 0.004 0.112
#> TCGA-02-0446-01A-01 4 0.2624 0.6124 0.000 0.000 0.012 0.872 0.116
#> TCGA-06-0128-01A-01 5 0.5297 0.3482 0.048 0.000 0.000 0.476 0.476
#> TCGA-06-0129-01A-01 1 0.2773 0.8089 0.836 0.000 0.000 0.000 0.164
#> TCGA-06-0146-01A-01 1 0.4219 0.3831 0.584 0.000 0.000 0.000 0.416
#> TCGA-06-0156-01A-01 4 0.2873 0.6029 0.000 0.000 0.016 0.856 0.128
#> TCGA-06-0166-01A-01 4 0.2777 0.6071 0.000 0.000 0.016 0.864 0.120
#> TCGA-06-0174-01A-01 1 0.2179 0.8492 0.896 0.000 0.000 0.004 0.100
#> TCGA-06-0177-01A-01 1 0.2074 0.8485 0.896 0.000 0.000 0.000 0.104
#> TCGA-06-0238-01A-02 5 0.5652 0.5207 0.088 0.000 0.000 0.360 0.552
#> TCGA-06-0241-01A-02 1 0.2124 0.8507 0.900 0.000 0.000 0.004 0.096
#> TCGA-06-0410-01A-01 1 0.2124 0.8507 0.900 0.000 0.000 0.004 0.096
#> TCGA-06-0413-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.2338 0.8442 0.884 0.000 0.000 0.004 0.112
#> TCGA-06-0646-01A-01 4 0.2727 0.6112 0.000 0.000 0.016 0.868 0.116
#> TCGA-06-0648-01A-01 1 0.2377 0.8375 0.872 0.000 0.000 0.000 0.128
#> TCGA-08-0245-01A-01 1 0.0671 0.8611 0.980 0.000 0.000 0.004 0.016
#> TCGA-08-0344-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 4 0.2864 0.5899 0.000 0.000 0.012 0.852 0.136
#> TCGA-08-0348-01A-01 1 0.6203 0.0444 0.464 0.000 0.000 0.140 0.396
#> TCGA-08-0350-01A-01 1 0.4304 0.2951 0.516 0.000 0.000 0.000 0.484
#> TCGA-08-0353-01A-01 3 0.0566 0.8847 0.000 0.000 0.984 0.004 0.012
#> TCGA-08-0359-01A-01 4 0.4251 -0.1063 0.004 0.000 0.000 0.624 0.372
#> TCGA-08-0385-01A-01 1 0.0510 0.8587 0.984 0.000 0.000 0.000 0.016
#> TCGA-08-0517-01A-01 1 0.1357 0.8603 0.948 0.000 0.000 0.004 0.048
#> TCGA-08-0524-01A-01 1 0.0000 0.8629 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.2124 0.8507 0.900 0.000 0.000 0.004 0.096
#> TCGA-12-0618-01A-01 1 0.1851 0.8540 0.912 0.000 0.000 0.000 0.088
#> TCGA-02-0089-01A-01 4 0.3707 0.5277 0.000 0.116 0.012 0.828 0.044
#> TCGA-02-0113-01A-01 3 0.5255 0.3600 0.000 0.000 0.560 0.388 0.052
#> TCGA-02-0115-01A-01 4 0.1410 0.6727 0.000 0.000 0.000 0.940 0.060
#> TCGA-02-0451-01A-01 4 0.0794 0.6634 0.000 0.000 0.000 0.972 0.028
#> TCGA-06-0132-01A-02 4 0.2605 0.6562 0.000 0.000 0.000 0.852 0.148
#> TCGA-06-0133-01A-02 4 0.2629 0.6505 0.000 0.000 0.004 0.860 0.136
#> TCGA-06-0138-01A-02 4 0.2233 0.6713 0.000 0.000 0.004 0.892 0.104
#> TCGA-06-0160-01A-01 4 0.4440 -0.2222 0.004 0.000 0.000 0.528 0.468
#> TCGA-06-0162-01A-01 4 0.2471 0.6514 0.000 0.000 0.000 0.864 0.136
#> TCGA-06-0167-01A-01 4 0.4440 -0.2222 0.004 0.000 0.000 0.528 0.468
#> TCGA-06-0171-01A-02 4 0.2389 0.6636 0.000 0.000 0.004 0.880 0.116
#> TCGA-06-0173-01A-01 4 0.1626 0.6522 0.000 0.000 0.016 0.940 0.044
#> TCGA-06-0179-01A-02 4 0.2605 0.6562 0.000 0.000 0.000 0.852 0.148
#> TCGA-06-0182-01A-01 3 0.5852 0.2739 0.000 0.000 0.524 0.372 0.104
#> TCGA-06-0185-01A-01 3 0.5682 0.3246 0.000 0.000 0.540 0.372 0.088
#> TCGA-06-0195-01B-01 4 0.3521 0.5270 0.004 0.000 0.000 0.764 0.232
#> TCGA-06-0208-01B-01 4 0.2677 0.6623 0.000 0.000 0.016 0.872 0.112
#> TCGA-06-0214-01A-02 4 0.1364 0.6561 0.000 0.000 0.012 0.952 0.036
#> TCGA-06-0219-01A-01 4 0.2674 0.6465 0.000 0.000 0.004 0.856 0.140
#> TCGA-06-0221-01A-01 4 0.4375 -0.0516 0.004 0.000 0.000 0.576 0.420
#> TCGA-06-0237-01A-02 4 0.2439 0.6593 0.000 0.000 0.004 0.876 0.120
#> TCGA-06-0240-01A-02 4 0.4299 0.0842 0.004 0.000 0.000 0.608 0.388
#> TCGA-08-0349-01A-01 4 0.1430 0.6724 0.000 0.000 0.004 0.944 0.052
#> TCGA-08-0380-01A-01 4 0.1851 0.6751 0.000 0.000 0.000 0.912 0.088
#> TCGA-08-0386-01A-01 3 0.5381 0.2442 0.000 0.000 0.516 0.428 0.056
#> TCGA-08-0520-01A-01 4 0.3970 0.5668 0.000 0.000 0.096 0.800 0.104
#> TCGA-02-0007-01A-01 3 0.5049 0.5331 0.000 0.000 0.644 0.296 0.060
#> TCGA-02-0009-01A-01 3 0.0000 0.8860 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.0703 0.8835 0.000 0.000 0.976 0.000 0.024
#> TCGA-02-0021-01A-01 3 0.0000 0.8860 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.1965 0.8653 0.000 0.000 0.904 0.000 0.096
#> TCGA-02-0027-01A-01 3 0.0771 0.8847 0.000 0.000 0.976 0.004 0.020
#> TCGA-02-0038-01A-01 4 0.6244 0.2484 0.000 0.072 0.276 0.600 0.052
#> TCGA-02-0043-01A-01 3 0.0162 0.8859 0.000 0.000 0.996 0.000 0.004
#> TCGA-02-0070-01A-01 3 0.0794 0.8831 0.000 0.000 0.972 0.000 0.028
#> TCGA-02-0102-01A-01 3 0.0510 0.8855 0.000 0.000 0.984 0.000 0.016
#> TCGA-02-0260-01A-03 3 0.2074 0.8464 0.000 0.000 0.896 0.000 0.104
#> TCGA-02-0269-01B-01 3 0.2074 0.8464 0.000 0.000 0.896 0.000 0.104
#> TCGA-02-0285-01A-01 3 0.0794 0.8831 0.000 0.000 0.972 0.000 0.028
#> TCGA-02-0289-01A-01 3 0.0609 0.8830 0.000 0.000 0.980 0.000 0.020
#> TCGA-02-0290-01A-01 3 0.0880 0.8809 0.000 0.000 0.968 0.000 0.032
#> TCGA-02-0317-01A-01 3 0.2074 0.8464 0.000 0.000 0.896 0.000 0.104
#> TCGA-02-0333-01A-02 3 0.2074 0.8464 0.000 0.000 0.896 0.000 0.104
#> TCGA-02-0422-01A-01 3 0.0510 0.8855 0.000 0.000 0.984 0.000 0.016
#> TCGA-02-0430-01A-01 3 0.0510 0.8855 0.000 0.000 0.984 0.000 0.016
#> TCGA-06-0125-01A-01 3 0.0000 0.8860 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.8860 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.0162 0.8862 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0145-01A-04 3 0.0609 0.8847 0.000 0.000 0.980 0.000 0.020
#> TCGA-06-0148-01A-01 3 0.0880 0.8809 0.000 0.000 0.968 0.000 0.032
#> TCGA-06-0187-01A-01 3 0.2628 0.8211 0.000 0.000 0.884 0.088 0.028
#> TCGA-06-0211-01B-01 3 0.0000 0.8860 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.8860 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.6369 0.4959 0.000 0.188 0.624 0.144 0.044
#> TCGA-08-0354-01A-01 3 0.1364 0.8812 0.000 0.000 0.952 0.012 0.036
#> TCGA-08-0355-01A-01 3 0.1965 0.8653 0.000 0.000 0.904 0.000 0.096
#> TCGA-08-0357-01A-01 3 0.0510 0.8855 0.000 0.000 0.984 0.000 0.016
#> TCGA-08-0358-01A-01 3 0.2074 0.8464 0.000 0.000 0.896 0.000 0.104
#> TCGA-08-0375-01A-01 3 0.0510 0.8836 0.000 0.000 0.984 0.000 0.016
#> TCGA-08-0511-01A-01 3 0.1403 0.8732 0.000 0.000 0.952 0.024 0.024
#> TCGA-08-0514-01A-01 3 0.1403 0.8732 0.000 0.000 0.952 0.024 0.024
#> TCGA-08-0518-01A-01 3 0.0162 0.8862 0.000 0.000 0.996 0.000 0.004
#> TCGA-08-0529-01A-02 3 0.0510 0.8855 0.000 0.000 0.984 0.000 0.016
#> TCGA-08-0531-01A-01 3 0.0162 0.8862 0.000 0.000 0.996 0.000 0.004
#> TCGA-02-0057-01A-01 4 0.5145 0.3282 0.000 0.256 0.012 0.676 0.056
#> TCGA-02-0004-01A-01 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-02-0006-01B-01 2 0.5390 0.1969 0.000 0.504 0.012 0.452 0.032
#> TCGA-02-0025-01A-01 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-02-0033-01A-01 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-02-0034-01A-01 2 0.3424 0.7506 0.000 0.760 0.000 0.000 0.240
#> TCGA-02-0039-01A-01 2 0.3400 0.7380 0.000 0.828 0.000 0.136 0.036
#> TCGA-02-0051-01A-01 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-02-0054-01A-01 2 0.5636 0.1878 0.000 0.496 0.012 0.444 0.048
#> TCGA-02-0055-01A-01 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-02-0059-01A-01 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-02-0064-01A-01 2 0.0510 0.8039 0.000 0.984 0.000 0.016 0.000
#> TCGA-02-0075-01A-01 2 0.0703 0.8049 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0079-01A-03 2 0.3239 0.7623 0.000 0.852 0.000 0.068 0.080
#> TCGA-02-0085-01A-01 4 0.3192 0.5422 0.000 0.112 0.000 0.848 0.040
#> TCGA-02-0086-01A-01 2 0.0671 0.8052 0.000 0.980 0.000 0.004 0.016
#> TCGA-02-0099-01A-01 2 0.5380 0.2292 0.000 0.516 0.012 0.440 0.032
#> TCGA-02-0106-01A-01 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-02-0107-01A-01 2 0.1549 0.7965 0.000 0.944 0.000 0.040 0.016
#> TCGA-02-0111-01A-01 2 0.0771 0.8032 0.000 0.976 0.000 0.020 0.004
#> TCGA-02-0326-01A-01 3 0.4088 0.5207 0.000 0.000 0.632 0.000 0.368
#> TCGA-02-0337-01A-01 2 0.4398 0.6316 0.000 0.720 0.000 0.240 0.040
#> TCGA-06-0122-01A-01 2 0.4185 0.7258 0.000 0.804 0.036 0.124 0.036
#> TCGA-06-0124-01A-01 2 0.0510 0.8039 0.000 0.984 0.000 0.016 0.000
#> TCGA-06-0130-01A-01 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-06-0139-01A-01 2 0.3039 0.7679 0.000 0.808 0.000 0.000 0.192
#> TCGA-06-0143-01A-01 2 0.4107 0.7236 0.000 0.804 0.024 0.132 0.040
#> TCGA-06-0147-01A-01 2 0.0880 0.8039 0.000 0.968 0.000 0.000 0.032
#> TCGA-06-0149-01A-05 2 0.5466 0.4435 0.000 0.600 0.012 0.336 0.052
#> TCGA-06-0152-01A-02 3 0.2424 0.8455 0.000 0.000 0.868 0.000 0.132
#> TCGA-06-0154-01A-02 2 0.0000 0.8044 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0671 0.8052 0.000 0.980 0.000 0.004 0.016
#> TCGA-06-0175-01A-01 2 0.5909 0.2856 0.000 0.524 0.028 0.400 0.048
#> TCGA-06-0176-01A-03 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-06-0184-01A-01 2 0.4800 0.4292 0.000 0.604 0.000 0.368 0.028
#> TCGA-06-0189-01A-05 2 0.3003 0.7691 0.000 0.812 0.000 0.000 0.188
#> TCGA-06-0190-01A-01 2 0.0510 0.8049 0.000 0.984 0.000 0.000 0.016
#> TCGA-06-0194-01A-01 2 0.0671 0.8052 0.000 0.980 0.000 0.004 0.016
#> TCGA-06-0197-01A-02 2 0.2852 0.7743 0.000 0.828 0.000 0.000 0.172
#> TCGA-06-0210-01A-01 2 0.1469 0.7979 0.000 0.948 0.000 0.036 0.016
#> TCGA-06-0397-01A-01 2 0.3561 0.7420 0.000 0.740 0.000 0.000 0.260
#> TCGA-06-0409-01A-02 2 0.0955 0.8015 0.000 0.968 0.000 0.028 0.004
#> TCGA-06-0412-01A-01 2 0.3248 0.7646 0.000 0.864 0.020 0.084 0.032
#> TCGA-06-0644-01A-02 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-06-0645-01A-01 2 0.2144 0.7854 0.000 0.912 0.000 0.068 0.020
#> TCGA-08-0346-01A-01 2 0.0771 0.8030 0.000 0.976 0.000 0.020 0.004
#> TCGA-08-0352-01A-01 2 0.3896 0.7318 0.000 0.816 0.020 0.128 0.036
#> TCGA-08-0360-01A-01 2 0.0865 0.8023 0.000 0.972 0.000 0.024 0.004
#> TCGA-08-0390-01A-01 2 0.2359 0.7950 0.000 0.904 0.000 0.060 0.036
#> TCGA-08-0392-01A-01 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-08-0509-01A-01 2 0.1626 0.7954 0.000 0.940 0.000 0.044 0.016
#> TCGA-08-0510-01A-01 2 0.2666 0.7771 0.000 0.892 0.020 0.076 0.012
#> TCGA-08-0512-01A-01 2 0.2377 0.7865 0.000 0.872 0.000 0.000 0.128
#> TCGA-08-0522-01A-01 2 0.3730 0.7284 0.000 0.712 0.000 0.000 0.288
#> TCGA-12-0619-01A-01 2 0.1732 0.7970 0.000 0.920 0.000 0.000 0.080
#> TCGA-12-0620-01A-01 2 0.4063 0.7387 0.000 0.820 0.040 0.096 0.044
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.5544 0.67747 0.656 0.000 0.000 0.112 0.172 0.060
#> TCGA-02-0010-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 5 0.4166 0.38919 0.324 0.000 0.000 0.028 0.648 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0146 0.83182 0.996 0.000 0.000 0.004 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.4980 0.72997 0.692 0.000 0.000 0.112 0.172 0.024
#> TCGA-02-0047-01A-01 6 0.5646 0.46294 0.000 0.016 0.004 0.188 0.180 0.612
#> TCGA-02-0048-01A-01 1 0.5944 0.68018 0.672 0.000 0.096 0.112 0.084 0.036
#> TCGA-02-0060-01A-01 5 0.4898 0.54231 0.032 0.000 0.000 0.076 0.696 0.196
#> TCGA-02-0069-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.4457 0.75562 0.720 0.000 0.000 0.108 0.168 0.004
#> TCGA-02-0080-01A-01 5 0.3619 0.49682 0.316 0.000 0.000 0.000 0.680 0.004
#> TCGA-02-0084-01A-03 5 0.3997 0.54329 0.000 0.060 0.000 0.020 0.780 0.140
#> TCGA-02-0087-01A-01 5 0.3352 0.59040 0.024 0.000 0.000 0.016 0.816 0.144
#> TCGA-02-0104-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.7506 0.08782 0.000 0.000 0.152 0.272 0.348 0.228
#> TCGA-02-0325-01A-01 5 0.5104 0.53850 0.184 0.000 0.032 0.080 0.696 0.008
#> TCGA-02-0338-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 5 0.3619 0.49682 0.316 0.000 0.000 0.000 0.680 0.004
#> TCGA-02-0439-01A-01 5 0.4400 0.49382 0.000 0.000 0.000 0.068 0.684 0.248
#> TCGA-02-0440-01A-01 1 0.4499 0.75273 0.716 0.000 0.000 0.112 0.168 0.004
#> TCGA-02-0446-01A-01 6 0.5722 0.45661 0.000 0.016 0.008 0.188 0.176 0.612
#> TCGA-06-0128-01A-01 5 0.5121 0.51917 0.032 0.000 0.000 0.068 0.652 0.248
#> TCGA-06-0129-01A-01 1 0.4163 0.70203 0.716 0.000 0.000 0.048 0.232 0.004
#> TCGA-06-0146-01A-01 5 0.3531 0.48114 0.328 0.000 0.000 0.000 0.672 0.000
#> TCGA-06-0156-01A-01 6 0.5611 0.45322 0.000 0.012 0.008 0.184 0.176 0.620
#> TCGA-06-0166-01A-01 6 0.5695 0.45279 0.000 0.016 0.008 0.184 0.176 0.616
#> TCGA-06-0174-01A-01 1 0.4293 0.77100 0.740 0.000 0.000 0.112 0.144 0.004
#> TCGA-06-0177-01A-01 1 0.4117 0.77297 0.752 0.000 0.000 0.084 0.160 0.004
#> TCGA-06-0238-01A-02 5 0.5626 0.56481 0.068 0.000 0.000 0.104 0.648 0.180
#> TCGA-06-0241-01A-02 1 0.4218 0.77599 0.748 0.000 0.000 0.112 0.136 0.004
#> TCGA-06-0410-01A-01 1 0.4423 0.77220 0.740 0.000 0.000 0.112 0.136 0.012
#> TCGA-06-0413-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.4499 0.75273 0.716 0.000 0.000 0.112 0.168 0.004
#> TCGA-06-0646-01A-01 6 0.5800 0.47332 0.000 0.028 0.008 0.188 0.156 0.620
#> TCGA-06-0648-01A-01 1 0.4513 0.72221 0.700 0.000 0.000 0.084 0.212 0.004
#> TCGA-08-0245-01A-01 1 0.1720 0.82441 0.928 0.000 0.000 0.040 0.032 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 6 0.5980 0.41994 0.000 0.020 0.008 0.192 0.200 0.580
#> TCGA-08-0348-01A-01 5 0.6478 0.49805 0.200 0.000 0.000 0.132 0.556 0.112
#> TCGA-08-0350-01A-01 5 0.3975 0.54190 0.204 0.000 0.000 0.048 0.744 0.004
#> TCGA-08-0353-01A-01 3 0.1408 0.85091 0.000 0.000 0.944 0.036 0.020 0.000
#> TCGA-08-0359-01A-01 5 0.5458 0.18319 0.000 0.000 0.000 0.124 0.480 0.396
#> TCGA-08-0385-01A-01 1 0.0713 0.81576 0.972 0.000 0.000 0.000 0.028 0.000
#> TCGA-08-0517-01A-01 1 0.3214 0.80825 0.836 0.000 0.000 0.080 0.080 0.004
#> TCGA-08-0524-01A-01 1 0.0000 0.83198 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.4326 0.77436 0.744 0.000 0.000 0.112 0.136 0.008
#> TCGA-12-0618-01A-01 1 0.3936 0.78480 0.772 0.000 0.000 0.084 0.140 0.004
#> TCGA-02-0089-01A-01 6 0.4367 0.56809 0.000 0.144 0.000 0.100 0.012 0.744
#> TCGA-02-0113-01A-01 3 0.5343 0.04842 0.000 0.000 0.472 0.072 0.012 0.444
#> TCGA-02-0115-01A-01 6 0.3320 0.63635 0.000 0.028 0.000 0.092 0.040 0.840
#> TCGA-02-0451-01A-01 6 0.3212 0.62685 0.000 0.048 0.000 0.100 0.012 0.840
#> TCGA-06-0132-01A-02 6 0.4139 0.58631 0.000 0.016 0.000 0.108 0.104 0.772
#> TCGA-06-0133-01A-02 6 0.3514 0.58530 0.000 0.000 0.000 0.088 0.108 0.804
#> TCGA-06-0138-01A-02 6 0.1873 0.64112 0.000 0.008 0.000 0.020 0.048 0.924
#> TCGA-06-0160-01A-01 5 0.5255 0.23299 0.000 0.000 0.000 0.112 0.548 0.340
#> TCGA-06-0162-01A-01 6 0.3657 0.58031 0.000 0.000 0.000 0.100 0.108 0.792
#> TCGA-06-0167-01A-01 5 0.5255 0.23299 0.000 0.000 0.000 0.112 0.548 0.340
#> TCGA-06-0171-01A-02 6 0.2325 0.62820 0.000 0.000 0.000 0.048 0.060 0.892
#> TCGA-06-0173-01A-01 6 0.4087 0.61423 0.000 0.024 0.016 0.128 0.040 0.792
#> TCGA-06-0179-01A-02 6 0.3820 0.58566 0.000 0.012 0.000 0.092 0.100 0.796
#> TCGA-06-0182-01A-01 6 0.5381 0.00667 0.000 0.000 0.436 0.056 0.024 0.484
#> TCGA-06-0185-01A-01 6 0.5236 -0.03706 0.000 0.000 0.452 0.044 0.024 0.480
#> TCGA-06-0195-01B-01 6 0.4636 0.48508 0.000 0.000 0.000 0.148 0.160 0.692
#> TCGA-06-0208-01B-01 6 0.3098 0.62387 0.000 0.000 0.032 0.056 0.052 0.860
#> TCGA-06-0214-01A-02 6 0.3190 0.62542 0.000 0.044 0.008 0.100 0.004 0.844
#> TCGA-06-0219-01A-01 6 0.3567 0.57936 0.000 0.000 0.000 0.100 0.100 0.800
#> TCGA-06-0221-01A-01 6 0.5248 0.12769 0.000 0.000 0.000 0.100 0.388 0.512
#> TCGA-06-0237-01A-02 6 0.2512 0.62266 0.000 0.000 0.000 0.060 0.060 0.880
#> TCGA-06-0240-01A-02 6 0.5347 0.21299 0.000 0.000 0.000 0.124 0.336 0.540
#> TCGA-08-0349-01A-01 6 0.2821 0.63734 0.000 0.000 0.004 0.096 0.040 0.860
#> TCGA-08-0380-01A-01 6 0.1605 0.64359 0.000 0.032 0.000 0.016 0.012 0.940
#> TCGA-08-0386-01A-01 3 0.6666 -0.15450 0.000 0.000 0.396 0.136 0.072 0.396
#> TCGA-08-0520-01A-01 6 0.3078 0.59975 0.000 0.000 0.084 0.032 0.028 0.856
#> TCGA-02-0007-01A-01 3 0.6616 0.14082 0.000 0.000 0.480 0.140 0.076 0.304
#> TCGA-02-0009-01A-01 3 0.0622 0.87004 0.000 0.000 0.980 0.008 0.012 0.000
#> TCGA-02-0016-01A-01 3 0.1572 0.86483 0.000 0.000 0.936 0.036 0.028 0.000
#> TCGA-02-0021-01A-01 3 0.0520 0.87042 0.000 0.000 0.984 0.008 0.008 0.000
#> TCGA-02-0023-01B-01 3 0.3356 0.83257 0.000 0.000 0.824 0.100 0.072 0.004
#> TCGA-02-0027-01A-01 3 0.1622 0.86966 0.000 0.000 0.940 0.028 0.016 0.016
#> TCGA-02-0038-01A-01 6 0.6232 0.48255 0.000 0.076 0.176 0.108 0.020 0.620
#> TCGA-02-0043-01A-01 3 0.1088 0.87049 0.000 0.000 0.960 0.016 0.024 0.000
#> TCGA-02-0070-01A-01 3 0.1765 0.85948 0.000 0.000 0.924 0.052 0.024 0.000
#> TCGA-02-0102-01A-01 3 0.0632 0.87094 0.000 0.000 0.976 0.024 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.3595 0.79496 0.000 0.000 0.796 0.084 0.120 0.000
#> TCGA-02-0269-01B-01 3 0.3595 0.79496 0.000 0.000 0.796 0.084 0.120 0.000
#> TCGA-02-0285-01A-01 3 0.1738 0.85843 0.000 0.000 0.928 0.052 0.016 0.004
#> TCGA-02-0289-01A-01 3 0.1492 0.86545 0.000 0.000 0.940 0.036 0.024 0.000
#> TCGA-02-0290-01A-01 3 0.2762 0.84360 0.000 0.000 0.860 0.092 0.048 0.000
#> TCGA-02-0317-01A-01 3 0.3595 0.79496 0.000 0.000 0.796 0.084 0.120 0.000
#> TCGA-02-0333-01A-02 3 0.3595 0.79496 0.000 0.000 0.796 0.084 0.120 0.000
#> TCGA-02-0422-01A-01 3 0.0777 0.86873 0.000 0.000 0.972 0.024 0.004 0.000
#> TCGA-02-0430-01A-01 3 0.0935 0.86768 0.000 0.000 0.964 0.032 0.004 0.000
#> TCGA-06-0125-01A-01 3 0.0717 0.86993 0.000 0.000 0.976 0.008 0.016 0.000
#> TCGA-06-0126-01A-01 3 0.0717 0.86993 0.000 0.000 0.976 0.008 0.016 0.000
#> TCGA-06-0137-01A-03 3 0.0820 0.86951 0.000 0.000 0.972 0.012 0.016 0.000
#> TCGA-06-0145-01A-04 3 0.1155 0.86645 0.000 0.000 0.956 0.036 0.004 0.004
#> TCGA-06-0148-01A-01 3 0.2712 0.84332 0.000 0.000 0.864 0.088 0.048 0.000
#> TCGA-06-0187-01A-01 3 0.3944 0.76149 0.000 0.008 0.804 0.096 0.020 0.072
#> TCGA-06-0211-01B-01 3 0.0622 0.87004 0.000 0.000 0.980 0.008 0.012 0.000
#> TCGA-06-0402-01A-01 3 0.0260 0.87083 0.000 0.000 0.992 0.008 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.6911 0.33842 0.000 0.232 0.528 0.124 0.020 0.096
#> TCGA-08-0354-01A-01 3 0.3851 0.81588 0.000 0.000 0.800 0.120 0.036 0.044
#> TCGA-08-0355-01A-01 3 0.3458 0.83032 0.000 0.000 0.820 0.104 0.068 0.008
#> TCGA-08-0357-01A-01 3 0.0891 0.86905 0.000 0.000 0.968 0.024 0.008 0.000
#> TCGA-08-0358-01A-01 3 0.3796 0.77968 0.000 0.000 0.776 0.084 0.140 0.000
#> TCGA-08-0375-01A-01 3 0.1418 0.86563 0.000 0.000 0.944 0.024 0.032 0.000
#> TCGA-08-0511-01A-01 3 0.1644 0.85983 0.000 0.000 0.932 0.052 0.012 0.004
#> TCGA-08-0514-01A-01 3 0.2123 0.84907 0.000 0.000 0.908 0.064 0.020 0.008
#> TCGA-08-0518-01A-01 3 0.0725 0.87123 0.000 0.000 0.976 0.012 0.012 0.000
#> TCGA-08-0529-01A-02 3 0.0935 0.86768 0.000 0.000 0.964 0.032 0.004 0.000
#> TCGA-08-0531-01A-01 3 0.0405 0.87103 0.000 0.000 0.988 0.004 0.008 0.000
#> TCGA-02-0057-01A-01 6 0.5971 0.29064 0.000 0.328 0.008 0.108 0.024 0.532
#> TCGA-02-0004-01A-01 4 0.3862 0.99499 0.000 0.476 0.000 0.524 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.5443 0.32400 0.000 0.552 0.008 0.092 0.004 0.344
#> TCGA-02-0025-01A-01 4 0.3862 0.99499 0.000 0.476 0.000 0.524 0.000 0.000
#> TCGA-02-0033-01A-01 4 0.3862 0.99499 0.000 0.476 0.000 0.524 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.3782 -0.71337 0.000 0.588 0.000 0.412 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.3410 0.62043 0.000 0.820 0.000 0.100 0.004 0.076
#> TCGA-02-0051-01A-01 4 0.4093 0.99298 0.000 0.476 0.000 0.516 0.008 0.000
#> TCGA-02-0054-01A-01 2 0.5960 0.18822 0.000 0.488 0.008 0.112 0.016 0.376
#> TCGA-02-0055-01A-01 4 0.3862 0.99499 0.000 0.476 0.000 0.524 0.000 0.000
#> TCGA-02-0059-01A-01 4 0.3862 0.99499 0.000 0.476 0.000 0.524 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.0547 0.62945 0.000 0.980 0.000 0.020 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.1686 0.57598 0.000 0.924 0.000 0.064 0.012 0.000
#> TCGA-02-0079-01A-03 2 0.3613 0.60660 0.000 0.828 0.000 0.056 0.064 0.052
#> TCGA-02-0085-01A-01 6 0.5406 0.44652 0.000 0.252 0.000 0.104 0.024 0.620
#> TCGA-02-0086-01A-01 2 0.1225 0.61063 0.000 0.952 0.000 0.036 0.012 0.000
#> TCGA-02-0099-01A-01 2 0.5534 0.21655 0.000 0.508 0.008 0.092 0.004 0.388
#> TCGA-02-0106-01A-01 4 0.4093 0.99298 0.000 0.476 0.000 0.516 0.008 0.000
#> TCGA-02-0107-01A-01 2 0.1080 0.64253 0.000 0.960 0.000 0.004 0.004 0.032
#> TCGA-02-0111-01A-01 2 0.0508 0.62953 0.000 0.984 0.000 0.012 0.004 0.000
#> TCGA-02-0326-01A-01 5 0.5297 0.03269 0.000 0.000 0.364 0.096 0.536 0.004
#> TCGA-02-0337-01A-01 2 0.5024 0.50067 0.000 0.676 0.000 0.104 0.020 0.200
#> TCGA-06-0122-01A-01 2 0.4353 0.59930 0.000 0.780 0.048 0.116 0.012 0.044
#> TCGA-06-0124-01A-01 2 0.1225 0.63520 0.000 0.952 0.000 0.036 0.012 0.000
#> TCGA-06-0130-01A-01 4 0.3862 0.99499 0.000 0.476 0.000 0.524 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.3601 -0.36565 0.000 0.684 0.000 0.312 0.004 0.000
#> TCGA-06-0143-01A-01 2 0.4279 0.59594 0.000 0.772 0.008 0.132 0.020 0.068
#> TCGA-06-0147-01A-01 2 0.1531 0.55981 0.000 0.928 0.000 0.068 0.004 0.000
#> TCGA-06-0149-01A-05 2 0.5617 0.48789 0.000 0.632 0.008 0.148 0.020 0.192
#> TCGA-06-0152-01A-02 3 0.4493 0.76376 0.000 0.000 0.720 0.132 0.144 0.004
#> TCGA-06-0154-01A-02 2 0.1867 0.61273 0.000 0.916 0.000 0.064 0.020 0.000
#> TCGA-06-0164-01A-01 2 0.0858 0.61416 0.000 0.968 0.000 0.028 0.004 0.000
#> TCGA-06-0175-01A-01 2 0.5906 0.47643 0.000 0.616 0.020 0.128 0.024 0.212
#> TCGA-06-0176-01A-03 4 0.3862 0.99499 0.000 0.476 0.000 0.524 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.4822 0.48770 0.000 0.656 0.000 0.092 0.004 0.248
#> TCGA-06-0189-01A-05 2 0.3741 -0.39389 0.000 0.672 0.000 0.320 0.008 0.000
#> TCGA-06-0190-01A-01 2 0.1462 0.57457 0.000 0.936 0.000 0.056 0.008 0.000
#> TCGA-06-0194-01A-01 2 0.0972 0.61195 0.000 0.964 0.000 0.028 0.008 0.000
#> TCGA-06-0197-01A-02 2 0.3421 -0.12353 0.000 0.736 0.000 0.256 0.008 0.000
#> TCGA-06-0210-01A-01 2 0.1480 0.64415 0.000 0.940 0.000 0.040 0.020 0.000
#> TCGA-06-0397-01A-01 2 0.4229 -0.80651 0.000 0.548 0.000 0.436 0.016 0.000
#> TCGA-06-0409-01A-02 2 0.0146 0.63901 0.000 0.996 0.000 0.004 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.3504 0.62226 0.000 0.824 0.020 0.124 0.020 0.012
#> TCGA-06-0644-01A-02 4 0.4093 0.99298 0.000 0.476 0.000 0.516 0.008 0.000
#> TCGA-06-0645-01A-01 2 0.2263 0.64769 0.000 0.900 0.000 0.060 0.004 0.036
#> TCGA-08-0346-01A-01 2 0.0806 0.63281 0.000 0.972 0.000 0.020 0.008 0.000
#> TCGA-08-0352-01A-01 2 0.3547 0.62301 0.000 0.820 0.008 0.116 0.008 0.048
#> TCGA-08-0360-01A-01 2 0.0260 0.63273 0.000 0.992 0.000 0.008 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.1738 0.64301 0.000 0.928 0.000 0.016 0.004 0.052
#> TCGA-08-0392-01A-01 4 0.4093 0.99298 0.000 0.476 0.000 0.516 0.008 0.000
#> TCGA-08-0509-01A-01 2 0.1401 0.64801 0.000 0.948 0.000 0.020 0.004 0.028
#> TCGA-08-0510-01A-01 2 0.2698 0.64019 0.000 0.872 0.008 0.096 0.020 0.004
#> TCGA-08-0512-01A-01 2 0.2669 0.34270 0.000 0.836 0.000 0.156 0.008 0.000
#> TCGA-08-0522-01A-01 4 0.4093 0.99298 0.000 0.476 0.000 0.516 0.008 0.000
#> TCGA-12-0619-01A-01 2 0.2450 0.45612 0.000 0.868 0.000 0.116 0.016 0.000
#> TCGA-12-0620-01A-01 2 0.4179 0.59601 0.000 0.788 0.020 0.124 0.048 0.020
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> MAD:kmeans 163 4.75e-21 2
#> MAD:kmeans 162 3.81e-51 3
#> MAD:kmeans 172 1.94e-71 4
#> MAD:kmeans 142 6.37e-67 5
#> MAD:kmeans 131 1.42e-71 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "skmeans"]
# you can also extract it by
# res = res_list["MAD:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.975 0.938 0.976 0.5031 0.498 0.498
#> 3 3 1.000 0.959 0.983 0.3199 0.748 0.536
#> 4 4 0.959 0.927 0.969 0.1230 0.868 0.634
#> 5 5 0.879 0.832 0.908 0.0502 0.933 0.751
#> 6 6 0.791 0.717 0.814 0.0414 0.975 0.886
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0048-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0084-01A-03 2 0.9996 0.0587 0.488 0.512
#> TCGA-02-0087-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0104-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0325-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.0672 0.9729 0.992 0.008
#> TCGA-06-0128-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0166-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0174-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.9522 0.4049 0.372 0.628
#> TCGA-06-0648-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0348-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0353-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.2236 0.9379 0.036 0.964
#> TCGA-02-0115-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.2043 0.9418 0.032 0.968
#> TCGA-06-0138-01A-02 2 0.3274 0.9148 0.060 0.940
#> TCGA-06-0160-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0171-01A-02 1 0.3733 0.9096 0.928 0.072
#> TCGA-06-0173-01A-01 2 0.1414 0.9526 0.020 0.980
#> TCGA-06-0179-01A-02 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.4431 0.8797 0.092 0.908
#> TCGA-06-0185-01A-01 1 0.8016 0.6683 0.756 0.244
#> TCGA-06-0195-01B-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.9933 0.1903 0.452 0.548
#> TCGA-06-0214-01A-02 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0219-01A-01 1 0.8327 0.6310 0.736 0.264
#> TCGA-06-0221-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0237-01A-02 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0240-01A-02 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0349-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0380-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0520-01A-01 2 0.5842 0.8238 0.140 0.860
#> TCGA-02-0007-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0009-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0016-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0021-01A-01 1 0.4022 0.9024 0.920 0.080
#> TCGA-02-0023-01B-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0038-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0043-01A-01 1 0.3879 0.9068 0.924 0.076
#> TCGA-02-0070-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0102-01A-01 1 0.8909 0.5511 0.692 0.308
#> TCGA-02-0260-01A-03 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0269-01B-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0285-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0289-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0290-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0317-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0333-01A-02 1 0.0000 0.9797 1.000 0.000
#> TCGA-02-0422-01A-01 2 0.9815 0.2764 0.420 0.580
#> TCGA-02-0430-01A-01 1 0.4815 0.8753 0.896 0.104
#> TCGA-06-0125-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0126-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0137-01A-03 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0145-01A-04 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0148-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0187-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0211-01B-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-06-0402-01A-01 1 0.9866 0.2266 0.568 0.432
#> TCGA-08-0246-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0357-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0358-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0375-01A-01 1 0.0000 0.9797 1.000 0.000
#> TCGA-08-0511-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0514-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0529-01A-02 2 0.0376 0.9663 0.004 0.996
#> TCGA-08-0531-01A-01 2 0.9977 0.1102 0.472 0.528
#> TCGA-02-0057-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-02-0326-01A-01 1 0.1184 0.9657 0.984 0.016
#> TCGA-02-0337-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9696 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9696 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.9696 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-02-0048-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0084-01A-03 2 0.5363 0.61500 0.276 0.724 0.000
#> TCGA-02-0087-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0104-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0325-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0439-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-02-0440-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-06-0128-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-06-0129-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-06-0166-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-06-0174-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 1 0.6057 0.47961 0.656 0.340 0.004
#> TCGA-06-0648-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-08-0347-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-08-0348-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-08-0353-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-08-0359-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-08-0385-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.98473 1.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.0237 0.98024 0.000 0.996 0.004
#> TCGA-02-0113-01A-01 3 0.0000 0.97719 0.000 0.000 1.000
#> TCGA-02-0115-01A-01 2 0.0237 0.98024 0.000 0.996 0.004
#> TCGA-02-0451-01A-01 2 0.0237 0.98024 0.000 0.996 0.004
#> TCGA-06-0132-01A-02 2 0.0237 0.98024 0.000 0.996 0.004
#> TCGA-06-0133-01A-02 2 0.6561 0.72605 0.144 0.756 0.100
#> TCGA-06-0138-01A-02 1 0.6126 0.45121 0.644 0.352 0.004
#> TCGA-06-0160-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-06-0162-01A-01 2 0.0237 0.98024 0.000 0.996 0.004
#> TCGA-06-0167-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-06-0171-01A-02 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-06-0173-01A-01 2 0.6521 -0.00136 0.492 0.504 0.004
#> TCGA-06-0179-01A-02 2 0.0237 0.98024 0.000 0.996 0.004
#> TCGA-06-0182-01A-01 3 0.0000 0.97719 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 3 0.0000 0.97719 0.000 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-06-0208-01B-01 3 0.0000 0.97719 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.0237 0.98024 0.000 0.996 0.004
#> TCGA-06-0219-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-06-0221-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-06-0237-01A-02 1 0.2537 0.90496 0.920 0.000 0.080
#> TCGA-06-0240-01A-02 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-08-0349-01A-01 1 0.0237 0.98300 0.996 0.000 0.004
#> TCGA-08-0380-01A-01 2 0.0237 0.98024 0.000 0.996 0.004
#> TCGA-08-0386-01A-01 3 0.5591 0.56162 0.304 0.000 0.696
#> TCGA-08-0520-01A-01 3 0.0237 0.97538 0.004 0.000 0.996
#> TCGA-02-0007-01A-01 3 0.6180 0.29814 0.416 0.000 0.584
#> TCGA-02-0009-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0016-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0021-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0023-01B-01 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-02-0027-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0038-01A-01 3 0.3340 0.85092 0.000 0.120 0.880
#> TCGA-02-0043-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0070-01A-01 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-02-0102-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0260-01A-03 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0269-01B-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0285-01A-01 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-02-0289-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0290-01A-01 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-02-0317-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0333-01A-02 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0422-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0430-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-06-0125-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-06-0126-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-06-0137-01A-03 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-06-0145-01A-04 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-06-0148-01A-01 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-06-0187-01A-01 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-06-0211-01B-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-06-0402-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-08-0246-01A-01 3 0.1529 0.94518 0.000 0.040 0.960
#> TCGA-08-0354-01A-01 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-08-0355-01A-01 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-08-0357-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-08-0358-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-08-0375-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-08-0511-01A-01 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-08-0514-01A-01 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-08-0518-01A-01 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-08-0529-01A-02 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-08-0531-01A-01 3 0.0000 0.97719 0.000 0.000 1.000
#> TCGA-02-0057-01A-01 2 0.0237 0.98024 0.000 0.996 0.004
#> TCGA-02-0004-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0054-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0079-01A-03 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0085-01A-01 2 0.0237 0.98024 0.000 0.996 0.004
#> TCGA-02-0086-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0099-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0106-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-02-0326-01A-01 3 0.0237 0.97864 0.004 0.000 0.996
#> TCGA-02-0337-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0122-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0124-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0143-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0152-01A-02 3 0.0237 0.97761 0.000 0.004 0.996
#> TCGA-06-0154-01A-02 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0412-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-08-0352-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-08-0392-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
#> TCGA-12-0620-01A-01 2 0.0000 0.98279 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-02-0048-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0084-01A-03 2 0.7058 0.297 0.168 0.560 0.000 0.272
#> TCGA-02-0087-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0104-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0325-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0439-01A-01 4 0.3907 0.725 0.232 0.000 0.000 0.768
#> TCGA-02-0440-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 4 0.4040 0.688 0.248 0.000 0.000 0.752
#> TCGA-06-0128-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-06-0156-01A-01 4 0.4907 0.359 0.420 0.000 0.000 0.580
#> TCGA-06-0166-01A-01 1 0.3356 0.765 0.824 0.000 0.000 0.176
#> TCGA-06-0174-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 4 0.4730 0.495 0.364 0.000 0.000 0.636
#> TCGA-06-0648-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 4 0.4746 0.487 0.368 0.000 0.000 0.632
#> TCGA-08-0348-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-08-0353-01A-01 3 0.3444 0.744 0.184 0.000 0.816 0.000
#> TCGA-08-0359-01A-01 4 0.4746 0.487 0.368 0.000 0.000 0.632
#> TCGA-08-0385-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.991 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-02-0113-01A-01 3 0.4961 0.254 0.000 0.000 0.552 0.448
#> TCGA-02-0115-01A-01 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-02-0451-01A-01 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0132-01A-02 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0133-01A-02 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 4 0.2011 0.858 0.080 0.000 0.000 0.920
#> TCGA-06-0162-01A-01 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 4 0.2011 0.858 0.080 0.000 0.000 0.920
#> TCGA-06-0171-01A-02 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0179-01A-02 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 3 0.4972 0.231 0.000 0.000 0.544 0.456
#> TCGA-06-0185-01A-01 3 0.4998 0.129 0.000 0.000 0.512 0.488
#> TCGA-06-0195-01B-01 4 0.0188 0.896 0.004 0.000 0.000 0.996
#> TCGA-06-0208-01B-01 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 4 0.3074 0.798 0.152 0.000 0.000 0.848
#> TCGA-06-0237-01A-02 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-08-0349-01A-01 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 4 0.0000 0.897 0.000 0.000 0.000 1.000
#> TCGA-08-0386-01A-01 4 0.3399 0.810 0.040 0.000 0.092 0.868
#> TCGA-08-0520-01A-01 4 0.0921 0.879 0.000 0.000 0.028 0.972
#> TCGA-02-0007-01A-01 1 0.4199 0.750 0.804 0.000 0.164 0.032
#> TCGA-02-0009-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0016-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0021-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0027-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0038-01A-01 4 0.0592 0.887 0.000 0.000 0.016 0.984
#> TCGA-02-0043-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-06-0137-01A-03 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-08-0246-01A-01 3 0.0336 0.951 0.000 0.008 0.992 0.000
#> TCGA-08-0354-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-08-0357-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-08-0358-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-08-0375-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0057-01A-01 4 0.3400 0.747 0.000 0.180 0.000 0.820
#> TCGA-02-0004-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0079-01A-03 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0085-01A-01 4 0.4477 0.539 0.000 0.312 0.000 0.688
#> TCGA-02-0086-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0106-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-02-0337-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0122-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0124-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.960 0.000 0.000 1.000 0.000
#> TCGA-06-0154-01A-02 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-08-0352-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-08-0392-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.0000 0.992 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.0510 0.89420 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0010-01A-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0011-01B-01 5 0.4074 0.63759 0.364 0.000 0.000 0.000 0.636
#> TCGA-02-0014-01A-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0024-01B-01 1 0.0290 0.89894 0.992 0.000 0.000 0.000 0.008
#> TCGA-02-0026-01B-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0028-01A-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0046-01A-01 1 0.0510 0.89420 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0047-01A-01 4 0.4696 0.26127 0.016 0.000 0.000 0.556 0.428
#> TCGA-02-0048-01A-01 1 0.0703 0.89915 0.976 0.000 0.000 0.000 0.024
#> TCGA-02-0060-01A-01 5 0.3336 0.77539 0.228 0.000 0.000 0.000 0.772
#> TCGA-02-0069-01A-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0074-01A-01 1 0.0609 0.89234 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0080-01A-01 5 0.3336 0.77613 0.228 0.000 0.000 0.000 0.772
#> TCGA-02-0084-01A-03 5 0.2152 0.69111 0.032 0.044 0.000 0.004 0.920
#> TCGA-02-0087-01A-01 5 0.2329 0.76079 0.124 0.000 0.000 0.000 0.876
#> TCGA-02-0104-01A-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0114-01A-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0281-01A-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0321-01A-01 1 0.3424 0.61846 0.760 0.000 0.000 0.000 0.240
#> TCGA-02-0325-01A-01 5 0.4060 0.57721 0.360 0.000 0.000 0.000 0.640
#> TCGA-02-0338-01A-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0339-01A-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0432-01A-02 5 0.3424 0.77333 0.240 0.000 0.000 0.000 0.760
#> TCGA-02-0439-01A-01 5 0.2654 0.68047 0.032 0.000 0.000 0.084 0.884
#> TCGA-02-0440-01A-01 1 0.0510 0.89420 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0446-01A-01 4 0.6206 0.29220 0.296 0.000 0.000 0.532 0.172
#> TCGA-06-0128-01A-01 5 0.4029 0.70556 0.316 0.000 0.000 0.004 0.680
#> TCGA-06-0129-01A-01 1 0.3074 0.66929 0.804 0.000 0.000 0.000 0.196
#> TCGA-06-0146-01A-01 5 0.3636 0.75470 0.272 0.000 0.000 0.000 0.728
#> TCGA-06-0156-01A-01 1 0.6150 -0.00233 0.464 0.000 0.000 0.404 0.132
#> TCGA-06-0166-01A-01 1 0.3865 0.69072 0.808 0.000 0.000 0.100 0.092
#> TCGA-06-0174-01A-01 1 0.0510 0.89420 0.984 0.000 0.000 0.000 0.016
#> TCGA-06-0177-01A-01 1 0.0404 0.89590 0.988 0.000 0.000 0.000 0.012
#> TCGA-06-0238-01A-02 5 0.3586 0.76186 0.264 0.000 0.000 0.000 0.736
#> TCGA-06-0241-01A-02 1 0.0510 0.89420 0.984 0.000 0.000 0.000 0.016
#> TCGA-06-0410-01A-01 1 0.0290 0.89705 0.992 0.000 0.000 0.000 0.008
#> TCGA-06-0413-01A-01 1 0.0162 0.89791 0.996 0.000 0.000 0.000 0.004
#> TCGA-06-0414-01A-01 1 0.0510 0.89420 0.984 0.000 0.000 0.000 0.016
#> TCGA-06-0646-01A-01 4 0.6319 0.27375 0.284 0.000 0.000 0.520 0.196
#> TCGA-06-0648-01A-01 1 0.2020 0.81762 0.900 0.000 0.000 0.000 0.100
#> TCGA-08-0245-01A-01 1 0.0290 0.89879 0.992 0.000 0.000 0.000 0.008
#> TCGA-08-0344-01A-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-08-0347-01A-01 5 0.5922 0.21177 0.112 0.000 0.000 0.368 0.520
#> TCGA-08-0348-01A-01 1 0.4283 -0.15476 0.544 0.000 0.000 0.000 0.456
#> TCGA-08-0350-01A-01 5 0.3707 0.73917 0.284 0.000 0.000 0.000 0.716
#> TCGA-08-0353-01A-01 1 0.4354 0.35631 0.624 0.000 0.368 0.000 0.008
#> TCGA-08-0359-01A-01 5 0.4748 0.60708 0.100 0.000 0.000 0.172 0.728
#> TCGA-08-0385-01A-01 1 0.1965 0.82199 0.904 0.000 0.000 0.000 0.096
#> TCGA-08-0517-01A-01 1 0.0609 0.89942 0.980 0.000 0.000 0.000 0.020
#> TCGA-08-0524-01A-01 1 0.0510 0.89940 0.984 0.000 0.000 0.000 0.016
#> TCGA-12-0616-01A-01 1 0.0000 0.89875 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0510 0.89925 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0089-01A-01 4 0.1952 0.75072 0.000 0.004 0.000 0.912 0.084
#> TCGA-02-0113-01A-01 4 0.4464 0.29236 0.000 0.000 0.408 0.584 0.008
#> TCGA-02-0115-01A-01 4 0.1671 0.75220 0.000 0.000 0.000 0.924 0.076
#> TCGA-02-0451-01A-01 4 0.1608 0.75320 0.000 0.000 0.000 0.928 0.072
#> TCGA-06-0132-01A-02 4 0.2020 0.74392 0.000 0.000 0.000 0.900 0.100
#> TCGA-06-0133-01A-02 4 0.0510 0.75773 0.000 0.000 0.000 0.984 0.016
#> TCGA-06-0138-01A-02 4 0.0404 0.75920 0.000 0.000 0.000 0.988 0.012
#> TCGA-06-0160-01A-01 5 0.3659 0.59102 0.012 0.000 0.000 0.220 0.768
#> TCGA-06-0162-01A-01 4 0.0510 0.75773 0.000 0.000 0.000 0.984 0.016
#> TCGA-06-0167-01A-01 5 0.3659 0.59102 0.012 0.000 0.000 0.220 0.768
#> TCGA-06-0171-01A-02 4 0.0162 0.75873 0.000 0.000 0.000 0.996 0.004
#> TCGA-06-0173-01A-01 4 0.1341 0.75509 0.000 0.000 0.000 0.944 0.056
#> TCGA-06-0179-01A-02 4 0.1608 0.75441 0.000 0.000 0.000 0.928 0.072
#> TCGA-06-0182-01A-01 4 0.4201 0.30037 0.000 0.000 0.408 0.592 0.000
#> TCGA-06-0185-01A-01 4 0.4415 0.33823 0.000 0.000 0.388 0.604 0.008
#> TCGA-06-0195-01B-01 4 0.3003 0.63885 0.000 0.000 0.000 0.812 0.188
#> TCGA-06-0208-01B-01 4 0.0290 0.75846 0.000 0.000 0.000 0.992 0.008
#> TCGA-06-0214-01A-02 4 0.1732 0.75115 0.000 0.000 0.000 0.920 0.080
#> TCGA-06-0219-01A-01 4 0.0510 0.75773 0.000 0.000 0.000 0.984 0.016
#> TCGA-06-0221-01A-01 4 0.4793 0.11858 0.020 0.000 0.000 0.544 0.436
#> TCGA-06-0237-01A-02 4 0.2020 0.71598 0.000 0.000 0.000 0.900 0.100
#> TCGA-06-0240-01A-02 4 0.3274 0.63600 0.000 0.000 0.000 0.780 0.220
#> TCGA-08-0349-01A-01 4 0.0510 0.75773 0.000 0.000 0.000 0.984 0.016
#> TCGA-08-0380-01A-01 4 0.1671 0.75686 0.000 0.000 0.000 0.924 0.076
#> TCGA-08-0386-01A-01 4 0.6644 0.48360 0.148 0.000 0.132 0.624 0.096
#> TCGA-08-0520-01A-01 4 0.2411 0.70782 0.000 0.000 0.008 0.884 0.108
#> TCGA-02-0007-01A-01 1 0.4943 0.66180 0.764 0.000 0.076 0.108 0.052
#> TCGA-02-0009-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.0703 0.96215 0.000 0.000 0.976 0.000 0.024
#> TCGA-02-0021-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.2179 0.91898 0.000 0.000 0.888 0.000 0.112
#> TCGA-02-0027-01A-01 3 0.0880 0.95824 0.000 0.000 0.968 0.000 0.032
#> TCGA-02-0038-01A-01 4 0.3085 0.72560 0.000 0.004 0.068 0.868 0.060
#> TCGA-02-0043-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.0451 0.96314 0.000 0.008 0.988 0.000 0.004
#> TCGA-02-0102-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.1732 0.94021 0.000 0.000 0.920 0.000 0.080
#> TCGA-02-0269-01B-01 3 0.1792 0.93818 0.000 0.000 0.916 0.000 0.084
#> TCGA-02-0285-01A-01 3 0.0794 0.96056 0.000 0.000 0.972 0.000 0.028
#> TCGA-02-0289-01A-01 3 0.0794 0.96131 0.000 0.000 0.972 0.000 0.028
#> TCGA-02-0290-01A-01 3 0.1671 0.94197 0.000 0.000 0.924 0.000 0.076
#> TCGA-02-0317-01A-01 3 0.1792 0.93818 0.000 0.000 0.916 0.000 0.084
#> TCGA-02-0333-01A-02 3 0.1792 0.93818 0.000 0.000 0.916 0.000 0.084
#> TCGA-02-0422-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.1608 0.94383 0.000 0.000 0.928 0.000 0.072
#> TCGA-06-0187-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.2548 0.86893 0.000 0.072 0.896 0.004 0.028
#> TCGA-08-0354-01A-01 3 0.2547 0.92912 0.000 0.016 0.900 0.016 0.068
#> TCGA-08-0355-01A-01 3 0.2230 0.91576 0.000 0.000 0.884 0.000 0.116
#> TCGA-08-0357-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0358-01A-01 3 0.2280 0.91241 0.000 0.000 0.880 0.000 0.120
#> TCGA-08-0375-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.96729 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0057-01A-01 4 0.5851 0.39883 0.000 0.288 0.000 0.580 0.132
#> TCGA-02-0004-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0006-01B-01 2 0.3741 0.81547 0.000 0.816 0.000 0.108 0.076
#> TCGA-02-0025-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0033-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0034-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0039-01A-01 2 0.0955 0.96723 0.000 0.968 0.000 0.004 0.028
#> TCGA-02-0051-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0054-01A-01 2 0.2069 0.93640 0.000 0.912 0.000 0.012 0.076
#> TCGA-02-0055-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0059-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0064-01A-01 2 0.0703 0.96927 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0075-01A-01 2 0.0290 0.97051 0.000 0.992 0.000 0.000 0.008
#> TCGA-02-0079-01A-03 2 0.2488 0.88669 0.000 0.872 0.000 0.004 0.124
#> TCGA-02-0085-01A-01 4 0.5960 0.31883 0.000 0.352 0.000 0.528 0.120
#> TCGA-02-0086-01A-01 2 0.0290 0.97051 0.000 0.992 0.000 0.000 0.008
#> TCGA-02-0099-01A-01 2 0.1942 0.93747 0.000 0.920 0.000 0.012 0.068
#> TCGA-02-0106-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0107-01A-01 2 0.0955 0.96723 0.000 0.968 0.000 0.004 0.028
#> TCGA-02-0111-01A-01 2 0.0794 0.96839 0.000 0.972 0.000 0.000 0.028
#> TCGA-02-0326-01A-01 5 0.2971 0.61360 0.008 0.000 0.156 0.000 0.836
#> TCGA-02-0337-01A-01 2 0.2735 0.89523 0.000 0.880 0.000 0.036 0.084
#> TCGA-06-0122-01A-01 2 0.0794 0.96839 0.000 0.972 0.000 0.000 0.028
#> TCGA-06-0124-01A-01 2 0.0510 0.97024 0.000 0.984 0.000 0.000 0.016
#> TCGA-06-0130-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-06-0139-01A-01 2 0.0290 0.97123 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0143-01A-01 2 0.0794 0.96839 0.000 0.972 0.000 0.000 0.028
#> TCGA-06-0147-01A-01 2 0.0703 0.96927 0.000 0.976 0.000 0.000 0.024
#> TCGA-06-0149-01A-05 2 0.0955 0.96723 0.000 0.968 0.000 0.004 0.028
#> TCGA-06-0152-01A-02 3 0.2329 0.90898 0.000 0.000 0.876 0.000 0.124
#> TCGA-06-0154-01A-02 2 0.0404 0.97093 0.000 0.988 0.000 0.000 0.012
#> TCGA-06-0164-01A-01 2 0.0162 0.97119 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0175-01A-01 2 0.0703 0.96927 0.000 0.976 0.000 0.000 0.024
#> TCGA-06-0176-01A-03 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-06-0184-01A-01 2 0.2409 0.91491 0.000 0.900 0.000 0.068 0.032
#> TCGA-06-0189-01A-05 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-06-0190-01A-01 2 0.0290 0.97051 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0194-01A-01 2 0.0000 0.97110 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0290 0.97051 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0210-01A-01 2 0.0609 0.96984 0.000 0.980 0.000 0.000 0.020
#> TCGA-06-0397-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-06-0409-01A-02 2 0.0794 0.96839 0.000 0.972 0.000 0.000 0.028
#> TCGA-06-0412-01A-01 2 0.0794 0.96839 0.000 0.972 0.000 0.000 0.028
#> TCGA-06-0644-01A-02 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-06-0645-01A-01 2 0.0794 0.96839 0.000 0.972 0.000 0.000 0.028
#> TCGA-08-0346-01A-01 2 0.0510 0.97024 0.000 0.984 0.000 0.000 0.016
#> TCGA-08-0352-01A-01 2 0.0955 0.96723 0.000 0.968 0.000 0.004 0.028
#> TCGA-08-0360-01A-01 2 0.0794 0.96839 0.000 0.972 0.000 0.000 0.028
#> TCGA-08-0390-01A-01 2 0.0566 0.97057 0.000 0.984 0.000 0.004 0.012
#> TCGA-08-0392-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-08-0509-01A-01 2 0.0955 0.96723 0.000 0.968 0.000 0.004 0.028
#> TCGA-08-0510-01A-01 2 0.0794 0.96839 0.000 0.972 0.000 0.000 0.028
#> TCGA-08-0512-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-08-0522-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-12-0619-01A-01 2 0.0703 0.96845 0.000 0.976 0.000 0.000 0.024
#> TCGA-12-0620-01A-01 2 0.1197 0.95633 0.000 0.952 0.000 0.000 0.048
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.1462 0.8859 0.936 0.000 0.000 0.000 0.008 0.056
#> TCGA-02-0010-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 5 0.3351 0.7091 0.288 0.000 0.000 0.000 0.712 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.1219 0.8936 0.948 0.000 0.000 0.000 0.004 0.048
#> TCGA-02-0047-01A-01 6 0.5907 0.2198 0.000 0.000 0.000 0.212 0.352 0.436
#> TCGA-02-0048-01A-01 1 0.0260 0.9121 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-02-0060-01A-01 5 0.3683 0.7761 0.160 0.000 0.000 0.004 0.784 0.052
#> TCGA-02-0069-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.1524 0.8820 0.932 0.000 0.000 0.000 0.008 0.060
#> TCGA-02-0080-01A-01 5 0.2527 0.7912 0.168 0.000 0.000 0.000 0.832 0.000
#> TCGA-02-0084-01A-03 5 0.1509 0.7109 0.012 0.008 0.000 0.008 0.948 0.024
#> TCGA-02-0087-01A-01 5 0.1728 0.7555 0.064 0.000 0.000 0.004 0.924 0.008
#> TCGA-02-0104-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.4707 0.5022 0.660 0.000 0.000 0.000 0.244 0.096
#> TCGA-02-0325-01A-01 5 0.3629 0.6530 0.260 0.000 0.000 0.000 0.724 0.016
#> TCGA-02-0338-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 5 0.2631 0.7903 0.180 0.000 0.000 0.000 0.820 0.000
#> TCGA-02-0439-01A-01 5 0.2959 0.6833 0.008 0.000 0.000 0.024 0.844 0.124
#> TCGA-02-0440-01A-01 1 0.1349 0.8883 0.940 0.000 0.000 0.000 0.004 0.056
#> TCGA-02-0446-01A-01 6 0.6916 0.3008 0.176 0.000 0.000 0.236 0.108 0.480
#> TCGA-06-0128-01A-01 5 0.3470 0.7757 0.200 0.000 0.000 0.028 0.772 0.000
#> TCGA-06-0129-01A-01 1 0.2882 0.7100 0.812 0.000 0.000 0.000 0.180 0.008
#> TCGA-06-0146-01A-01 5 0.2823 0.7815 0.204 0.000 0.000 0.000 0.796 0.000
#> TCGA-06-0156-01A-01 6 0.7270 0.2474 0.312 0.000 0.000 0.216 0.108 0.364
#> TCGA-06-0166-01A-01 1 0.5436 0.1904 0.540 0.000 0.000 0.052 0.036 0.372
#> TCGA-06-0174-01A-01 1 0.0692 0.9084 0.976 0.000 0.000 0.000 0.004 0.020
#> TCGA-06-0177-01A-01 1 0.1196 0.8958 0.952 0.000 0.000 0.000 0.008 0.040
#> TCGA-06-0238-01A-02 5 0.3836 0.7317 0.252 0.000 0.000 0.012 0.724 0.012
#> TCGA-06-0241-01A-02 1 0.0508 0.9118 0.984 0.000 0.000 0.000 0.004 0.012
#> TCGA-06-0410-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.1265 0.8932 0.948 0.000 0.000 0.000 0.008 0.044
#> TCGA-06-0646-01A-01 6 0.6697 0.3240 0.128 0.000 0.000 0.244 0.116 0.512
#> TCGA-06-0648-01A-01 1 0.1075 0.8814 0.952 0.000 0.000 0.000 0.048 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0146 0.9155 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-08-0347-01A-01 6 0.6445 0.1513 0.044 0.000 0.000 0.152 0.376 0.428
#> TCGA-08-0348-01A-01 1 0.5412 -0.0736 0.496 0.000 0.000 0.000 0.384 0.120
#> TCGA-08-0350-01A-01 5 0.2823 0.7785 0.204 0.000 0.000 0.000 0.796 0.000
#> TCGA-08-0353-01A-01 3 0.3966 0.1406 0.444 0.000 0.552 0.000 0.000 0.004
#> TCGA-08-0359-01A-01 5 0.5672 0.3390 0.036 0.000 0.000 0.096 0.584 0.284
#> TCGA-08-0385-01A-01 1 0.1007 0.8852 0.956 0.000 0.000 0.000 0.044 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.9173 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0146 0.9155 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0089-01A-01 4 0.3795 0.4739 0.000 0.000 0.000 0.632 0.004 0.364
#> TCGA-02-0113-01A-01 4 0.3892 0.5422 0.000 0.000 0.212 0.740 0.000 0.048
#> TCGA-02-0115-01A-01 4 0.3684 0.5202 0.000 0.000 0.000 0.664 0.004 0.332
#> TCGA-02-0451-01A-01 4 0.3707 0.5284 0.000 0.000 0.000 0.680 0.008 0.312
#> TCGA-06-0132-01A-02 4 0.4249 0.4856 0.000 0.000 0.000 0.640 0.032 0.328
#> TCGA-06-0133-01A-02 4 0.0000 0.7034 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0138-01A-02 4 0.2100 0.6782 0.000 0.000 0.000 0.884 0.004 0.112
#> TCGA-06-0160-01A-01 5 0.3551 0.6513 0.000 0.000 0.000 0.168 0.784 0.048
#> TCGA-06-0162-01A-01 4 0.0000 0.7034 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0167-01A-01 5 0.3551 0.6513 0.000 0.000 0.000 0.168 0.784 0.048
#> TCGA-06-0171-01A-02 4 0.1152 0.6981 0.000 0.000 0.000 0.952 0.004 0.044
#> TCGA-06-0173-01A-01 4 0.3778 0.5439 0.000 0.000 0.000 0.696 0.016 0.288
#> TCGA-06-0179-01A-02 4 0.3595 0.5613 0.000 0.000 0.000 0.704 0.008 0.288
#> TCGA-06-0182-01A-01 4 0.3885 0.5261 0.000 0.000 0.220 0.736 0.000 0.044
#> TCGA-06-0185-01A-01 4 0.3587 0.5642 0.000 0.000 0.188 0.772 0.000 0.040
#> TCGA-06-0195-01B-01 4 0.2547 0.6528 0.004 0.000 0.000 0.868 0.112 0.016
#> TCGA-06-0208-01B-01 4 0.0363 0.7024 0.000 0.000 0.000 0.988 0.000 0.012
#> TCGA-06-0214-01A-02 4 0.3992 0.4549 0.000 0.000 0.000 0.624 0.012 0.364
#> TCGA-06-0219-01A-01 4 0.0000 0.7034 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0221-01A-01 4 0.4058 0.3347 0.004 0.000 0.000 0.616 0.372 0.008
#> TCGA-06-0237-01A-02 4 0.1367 0.6908 0.000 0.000 0.000 0.944 0.044 0.012
#> TCGA-06-0240-01A-02 4 0.3830 0.5794 0.000 0.000 0.000 0.744 0.212 0.044
#> TCGA-08-0349-01A-01 4 0.0717 0.7001 0.000 0.000 0.000 0.976 0.008 0.016
#> TCGA-08-0380-01A-01 4 0.2933 0.6340 0.000 0.000 0.000 0.796 0.004 0.200
#> TCGA-08-0386-01A-01 4 0.6635 0.3976 0.092 0.000 0.212 0.580 0.040 0.076
#> TCGA-08-0520-01A-01 4 0.2614 0.6709 0.000 0.000 0.012 0.884 0.060 0.044
#> TCGA-02-0007-01A-01 1 0.6641 0.2305 0.504 0.000 0.116 0.308 0.020 0.052
#> TCGA-02-0009-01A-01 3 0.0146 0.8695 0.000 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0016-01A-01 3 0.2542 0.8522 0.000 0.000 0.876 0.000 0.044 0.080
#> TCGA-02-0021-01A-01 3 0.0260 0.8700 0.000 0.000 0.992 0.000 0.000 0.008
#> TCGA-02-0023-01B-01 3 0.5029 0.7580 0.000 0.000 0.680 0.016 0.152 0.152
#> TCGA-02-0027-01A-01 3 0.1592 0.8614 0.000 0.000 0.940 0.008 0.020 0.032
#> TCGA-02-0038-01A-01 4 0.5460 0.3524 0.000 0.000 0.116 0.524 0.004 0.356
#> TCGA-02-0043-01A-01 3 0.0547 0.8697 0.000 0.000 0.980 0.000 0.000 0.020
#> TCGA-02-0070-01A-01 3 0.1584 0.8555 0.000 0.000 0.928 0.000 0.008 0.064
#> TCGA-02-0102-01A-01 3 0.0458 0.8697 0.000 0.000 0.984 0.000 0.000 0.016
#> TCGA-02-0260-01A-03 3 0.4124 0.7908 0.000 0.000 0.748 0.000 0.132 0.120
#> TCGA-02-0269-01B-01 3 0.4164 0.7886 0.000 0.000 0.744 0.000 0.132 0.124
#> TCGA-02-0285-01A-01 3 0.3123 0.8393 0.000 0.000 0.824 0.000 0.040 0.136
#> TCGA-02-0289-01A-01 3 0.2697 0.8468 0.000 0.000 0.864 0.000 0.044 0.092
#> TCGA-02-0290-01A-01 3 0.4853 0.7760 0.000 0.012 0.692 0.000 0.124 0.172
#> TCGA-02-0317-01A-01 3 0.4242 0.7838 0.000 0.000 0.736 0.000 0.136 0.128
#> TCGA-02-0333-01A-02 3 0.4279 0.7812 0.000 0.000 0.732 0.000 0.140 0.128
#> TCGA-02-0422-01A-01 3 0.0363 0.8699 0.000 0.000 0.988 0.000 0.000 0.012
#> TCGA-02-0430-01A-01 3 0.0547 0.8697 0.000 0.000 0.980 0.000 0.000 0.020
#> TCGA-06-0125-01A-01 3 0.0000 0.8699 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.0291 0.8702 0.000 0.000 0.992 0.000 0.004 0.004
#> TCGA-06-0137-01A-03 3 0.0692 0.8702 0.000 0.000 0.976 0.000 0.004 0.020
#> TCGA-06-0145-01A-04 3 0.0937 0.8671 0.000 0.000 0.960 0.000 0.000 0.040
#> TCGA-06-0148-01A-01 3 0.4226 0.7986 0.000 0.000 0.736 0.000 0.112 0.152
#> TCGA-06-0187-01A-01 3 0.2070 0.8370 0.000 0.000 0.892 0.000 0.008 0.100
#> TCGA-06-0211-01B-01 3 0.0260 0.8702 0.000 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0402-01A-01 3 0.0547 0.8697 0.000 0.000 0.980 0.000 0.000 0.020
#> TCGA-08-0246-01A-01 3 0.6067 0.2544 0.000 0.132 0.500 0.012 0.012 0.344
#> TCGA-08-0354-01A-01 3 0.6245 0.7161 0.000 0.052 0.612 0.032 0.100 0.204
#> TCGA-08-0355-01A-01 3 0.5110 0.7544 0.000 0.000 0.676 0.020 0.156 0.148
#> TCGA-08-0357-01A-01 3 0.0363 0.8686 0.000 0.000 0.988 0.000 0.000 0.012
#> TCGA-08-0358-01A-01 3 0.4387 0.7726 0.000 0.000 0.720 0.000 0.152 0.128
#> TCGA-08-0375-01A-01 3 0.0790 0.8706 0.000 0.000 0.968 0.000 0.000 0.032
#> TCGA-08-0511-01A-01 3 0.0935 0.8672 0.000 0.000 0.964 0.000 0.004 0.032
#> TCGA-08-0514-01A-01 3 0.1866 0.8518 0.000 0.000 0.908 0.000 0.008 0.084
#> TCGA-08-0518-01A-01 3 0.1049 0.8716 0.000 0.000 0.960 0.000 0.008 0.032
#> TCGA-08-0529-01A-02 3 0.0547 0.8695 0.000 0.000 0.980 0.000 0.000 0.020
#> TCGA-08-0531-01A-01 3 0.0603 0.8699 0.000 0.000 0.980 0.000 0.004 0.016
#> TCGA-02-0057-01A-01 6 0.5596 0.3028 0.000 0.120 0.000 0.260 0.024 0.596
#> TCGA-02-0004-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-02-0006-01B-01 6 0.4597 -0.0837 0.000 0.412 0.000 0.040 0.000 0.548
#> TCGA-02-0025-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-02-0033-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-02-0034-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-02-0039-01A-01 2 0.3337 0.7410 0.000 0.736 0.000 0.000 0.004 0.260
#> TCGA-02-0051-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-02-0054-01A-01 2 0.4491 0.4045 0.000 0.516 0.000 0.012 0.012 0.460
#> TCGA-02-0055-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-02-0059-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-02-0064-01A-01 2 0.2994 0.7780 0.000 0.788 0.000 0.000 0.004 0.208
#> TCGA-02-0075-01A-01 2 0.1757 0.8127 0.000 0.916 0.000 0.000 0.008 0.076
#> TCGA-02-0079-01A-03 2 0.4913 0.6211 0.000 0.636 0.000 0.000 0.112 0.252
#> TCGA-02-0085-01A-01 6 0.5906 0.3461 0.000 0.152 0.000 0.256 0.028 0.564
#> TCGA-02-0086-01A-01 2 0.0790 0.8128 0.000 0.968 0.000 0.000 0.000 0.032
#> TCGA-02-0099-01A-01 2 0.4492 0.2142 0.000 0.496 0.000 0.008 0.016 0.480
#> TCGA-02-0106-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-02-0107-01A-01 2 0.3383 0.7355 0.000 0.728 0.000 0.000 0.004 0.268
#> TCGA-02-0111-01A-01 2 0.2703 0.7922 0.000 0.824 0.000 0.000 0.004 0.172
#> TCGA-02-0326-01A-01 5 0.3865 0.5638 0.000 0.000 0.076 0.008 0.784 0.132
#> TCGA-02-0337-01A-01 6 0.4864 -0.2010 0.000 0.464 0.000 0.016 0.028 0.492
#> TCGA-06-0122-01A-01 2 0.3512 0.7416 0.000 0.720 0.000 0.000 0.008 0.272
#> TCGA-06-0124-01A-01 2 0.2848 0.7930 0.000 0.816 0.000 0.000 0.008 0.176
#> TCGA-06-0130-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-06-0139-01A-01 2 0.1588 0.8136 0.000 0.924 0.000 0.000 0.004 0.072
#> TCGA-06-0143-01A-01 2 0.3595 0.7312 0.000 0.704 0.000 0.000 0.008 0.288
#> TCGA-06-0147-01A-01 2 0.2738 0.7904 0.000 0.820 0.000 0.000 0.004 0.176
#> TCGA-06-0149-01A-05 2 0.4179 0.6750 0.000 0.652 0.000 0.008 0.016 0.324
#> TCGA-06-0152-01A-02 3 0.5410 0.7286 0.000 0.008 0.628 0.004 0.168 0.192
#> TCGA-06-0154-01A-02 2 0.1802 0.8074 0.000 0.916 0.000 0.000 0.012 0.072
#> TCGA-06-0164-01A-01 2 0.2003 0.8077 0.000 0.884 0.000 0.000 0.000 0.116
#> TCGA-06-0175-01A-01 2 0.3271 0.7686 0.000 0.760 0.000 0.000 0.008 0.232
#> TCGA-06-0176-01A-03 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-06-0184-01A-01 2 0.5150 0.5267 0.000 0.588 0.000 0.096 0.004 0.312
#> TCGA-06-0189-01A-05 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-06-0190-01A-01 2 0.0891 0.8104 0.000 0.968 0.000 0.000 0.008 0.024
#> TCGA-06-0194-01A-01 2 0.1204 0.8128 0.000 0.944 0.000 0.000 0.000 0.056
#> TCGA-06-0197-01A-02 2 0.0806 0.8057 0.000 0.972 0.000 0.000 0.008 0.020
#> TCGA-06-0210-01A-01 2 0.2848 0.7926 0.000 0.816 0.000 0.000 0.008 0.176
#> TCGA-06-0397-01A-01 2 0.2060 0.7874 0.000 0.900 0.000 0.000 0.016 0.084
#> TCGA-06-0409-01A-02 2 0.3081 0.7709 0.000 0.776 0.000 0.000 0.004 0.220
#> TCGA-06-0412-01A-01 2 0.3373 0.7609 0.000 0.744 0.000 0.000 0.008 0.248
#> TCGA-06-0644-01A-02 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-06-0645-01A-01 2 0.3349 0.7555 0.000 0.748 0.000 0.000 0.008 0.244
#> TCGA-08-0346-01A-01 2 0.2191 0.8056 0.000 0.876 0.000 0.000 0.004 0.120
#> TCGA-08-0352-01A-01 2 0.3710 0.7198 0.000 0.696 0.000 0.000 0.012 0.292
#> TCGA-08-0360-01A-01 2 0.2838 0.7862 0.000 0.808 0.000 0.000 0.004 0.188
#> TCGA-08-0390-01A-01 2 0.2278 0.8086 0.000 0.868 0.000 0.000 0.004 0.128
#> TCGA-08-0392-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-08-0509-01A-01 2 0.3314 0.7451 0.000 0.740 0.000 0.000 0.004 0.256
#> TCGA-08-0510-01A-01 2 0.3373 0.7595 0.000 0.744 0.000 0.000 0.008 0.248
#> TCGA-08-0512-01A-01 2 0.1838 0.7976 0.000 0.916 0.000 0.000 0.016 0.068
#> TCGA-08-0522-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-12-0619-01A-01 2 0.2006 0.7885 0.000 0.904 0.000 0.000 0.016 0.080
#> TCGA-12-0620-01A-01 2 0.3806 0.7372 0.000 0.752 0.000 0.000 0.048 0.200
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> MAD:skmeans 167 2.00e-22 2
#> MAD:skmeans 169 1.15e-54 3
#> MAD:skmeans 165 1.92e-83 4
#> MAD:skmeans 159 7.03e-84 5
#> MAD:skmeans 150 2.72e-82 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "pam"]
# you can also extract it by
# res = res_list["MAD:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.928 0.940 0.974 0.4128 0.582 0.582
#> 3 3 0.779 0.874 0.945 0.5687 0.767 0.600
#> 4 4 0.774 0.808 0.918 0.1457 0.851 0.606
#> 5 5 0.727 0.670 0.852 0.0371 0.984 0.937
#> 6 6 0.712 0.622 0.830 0.0194 0.975 0.901
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.1414 0.929 0.980 0.020
#> TCGA-02-0047-01A-01 1 0.9954 0.164 0.540 0.460
#> TCGA-02-0048-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.8016 0.713 0.756 0.244
#> TCGA-02-0084-01A-03 2 0.0672 0.979 0.008 0.992
#> TCGA-02-0087-01A-01 1 0.8144 0.701 0.748 0.252
#> TCGA-02-0104-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.9815 0.356 0.580 0.420
#> TCGA-02-0325-01A-01 1 0.8144 0.701 0.748 0.252
#> TCGA-02-0338-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.7528 0.751 0.784 0.216
#> TCGA-02-0440-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0446-01A-01 2 0.9963 0.106 0.464 0.536
#> TCGA-06-0128-01A-01 1 0.6247 0.807 0.844 0.156
#> TCGA-06-0129-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-06-0156-01A-01 2 0.8327 0.627 0.264 0.736
#> TCGA-06-0166-01A-01 2 0.8207 0.640 0.256 0.744
#> TCGA-06-0174-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-06-0238-01A-02 1 0.7056 0.779 0.808 0.192
#> TCGA-06-0241-01A-02 1 0.0000 0.942 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0648-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-08-0347-01A-01 2 0.9393 0.433 0.356 0.644
#> TCGA-08-0348-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.8016 0.713 0.756 0.244
#> TCGA-08-0353-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0359-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.7219 0.772 0.800 0.200
#> TCGA-12-0618-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0115-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.0672 0.979 0.008 0.992
#> TCGA-06-0133-01A-02 2 0.0672 0.979 0.008 0.992
#> TCGA-06-0138-01A-02 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.0672 0.979 0.008 0.992
#> TCGA-06-0167-01A-01 1 0.0000 0.942 1.000 0.000
#> TCGA-06-0171-01A-02 2 0.0672 0.979 0.008 0.992
#> TCGA-06-0173-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0179-01A-02 2 0.0672 0.979 0.008 0.992
#> TCGA-06-0182-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0185-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.0000 0.942 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.4431 0.887 0.092 0.908
#> TCGA-06-0221-01A-01 1 0.5629 0.840 0.868 0.132
#> TCGA-06-0237-01A-02 2 0.0672 0.979 0.008 0.992
#> TCGA-06-0240-01A-02 1 0.0000 0.942 1.000 0.000
#> TCGA-08-0349-01A-01 2 0.0672 0.979 0.008 0.992
#> TCGA-08-0380-01A-01 2 0.0672 0.979 0.008 0.992
#> TCGA-08-0386-01A-01 2 0.4431 0.886 0.092 0.908
#> TCGA-08-0520-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0007-01A-01 2 0.2236 0.950 0.036 0.964
#> TCGA-02-0009-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0016-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0021-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0023-01B-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0027-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0038-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0043-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0070-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0102-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0260-01A-03 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0269-01B-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0285-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0289-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0290-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0317-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0333-01A-02 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0422-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0430-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0125-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0126-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0137-01A-03 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0145-01A-04 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0148-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0187-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0211-01B-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0402-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0246-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0357-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0358-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0375-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0511-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0514-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0529-01A-02 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0531-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0057-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0672 0.979 0.008 0.992
#> TCGA-02-0086-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.2043 0.955 0.032 0.968
#> TCGA-02-0337-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0147-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.985 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.985 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.985 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.1163 0.9144 0.972 0.000 0.028
#> TCGA-02-0047-01A-01 1 0.9112 0.3490 0.524 0.168 0.308
#> TCGA-02-0048-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.4931 0.7247 0.768 0.000 0.232
#> TCGA-02-0084-01A-03 3 0.0424 0.9402 0.008 0.000 0.992
#> TCGA-02-0087-01A-01 1 0.4974 0.7189 0.764 0.000 0.236
#> TCGA-02-0104-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.6180 0.3555 0.584 0.000 0.416
#> TCGA-02-0325-01A-01 1 0.4974 0.7189 0.764 0.000 0.236
#> TCGA-02-0338-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0439-01A-01 1 0.4605 0.7617 0.796 0.000 0.204
#> TCGA-02-0440-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 2 0.6565 0.3073 0.416 0.576 0.008
#> TCGA-06-0128-01A-01 1 0.4178 0.7764 0.828 0.000 0.172
#> TCGA-06-0129-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 3 0.7091 0.5995 0.248 0.064 0.688
#> TCGA-06-0166-01A-01 3 0.5016 0.6685 0.240 0.000 0.760
#> TCGA-06-0174-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.4452 0.7739 0.808 0.000 0.192
#> TCGA-06-0241-01A-02 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0648-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-08-0347-01A-01 3 0.5835 0.4879 0.340 0.000 0.660
#> TCGA-08-0348-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-08-0350-01A-01 1 0.4931 0.7248 0.768 0.000 0.232
#> TCGA-08-0353-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0359-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.4555 0.7679 0.800 0.000 0.200
#> TCGA-12-0618-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-02-0089-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0113-01A-01 3 0.1411 0.9194 0.000 0.036 0.964
#> TCGA-02-0115-01A-01 2 0.4346 0.7971 0.000 0.816 0.184
#> TCGA-02-0451-01A-01 2 0.4121 0.8157 0.000 0.832 0.168
#> TCGA-06-0132-01A-02 2 0.3896 0.8506 0.008 0.864 0.128
#> TCGA-06-0133-01A-02 3 0.4531 0.7613 0.008 0.168 0.824
#> TCGA-06-0138-01A-02 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-06-0162-01A-01 2 0.3896 0.8506 0.008 0.864 0.128
#> TCGA-06-0167-01A-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-06-0171-01A-02 3 0.0424 0.9402 0.008 0.000 0.992
#> TCGA-06-0173-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0179-01A-02 2 0.3896 0.8506 0.008 0.864 0.128
#> TCGA-06-0182-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-06-0208-01B-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 3 0.8297 0.2974 0.092 0.348 0.560
#> TCGA-06-0221-01A-01 1 0.3551 0.8290 0.868 0.000 0.132
#> TCGA-06-0237-01A-02 3 0.0424 0.9402 0.008 0.000 0.992
#> TCGA-06-0240-01A-02 1 0.0000 0.9349 1.000 0.000 0.000
#> TCGA-08-0349-01A-01 3 0.0424 0.9402 0.008 0.000 0.992
#> TCGA-08-0380-01A-01 2 0.3896 0.8506 0.008 0.864 0.128
#> TCGA-08-0386-01A-01 3 0.2796 0.8628 0.092 0.000 0.908
#> TCGA-08-0520-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.1411 0.9172 0.036 0.000 0.964
#> TCGA-02-0009-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0016-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0021-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0023-01B-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0027-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0038-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0043-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0070-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0102-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0260-01A-03 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0269-01B-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0285-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0289-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0290-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0317-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0333-01A-02 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0422-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0430-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0125-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0126-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0137-01A-03 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0145-01A-04 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0148-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0187-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0211-01B-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0402-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0246-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0354-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0355-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0357-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0358-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0375-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0511-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0514-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0518-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0529-01A-02 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0531-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-02-0057-01A-01 3 0.0237 0.9431 0.000 0.004 0.996
#> TCGA-02-0004-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.3619 0.8469 0.000 0.864 0.136
#> TCGA-02-0025-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-02-0054-01A-01 2 0.5016 0.7215 0.000 0.760 0.240
#> TCGA-02-0055-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 2 0.5926 0.4336 0.000 0.644 0.356
#> TCGA-02-0075-01A-01 2 0.1529 0.8996 0.000 0.960 0.040
#> TCGA-02-0079-01A-03 3 0.3482 0.8251 0.000 0.128 0.872
#> TCGA-02-0085-01A-01 3 0.6664 0.0507 0.008 0.464 0.528
#> TCGA-02-0086-01A-01 2 0.0237 0.9208 0.000 0.996 0.004
#> TCGA-02-0099-01A-01 2 0.3619 0.8469 0.000 0.864 0.136
#> TCGA-02-0106-01A-01 3 0.3619 0.8157 0.000 0.136 0.864
#> TCGA-02-0107-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-02-0326-01A-01 3 0.1289 0.9214 0.032 0.000 0.968
#> TCGA-02-0337-01A-01 3 0.1031 0.9284 0.000 0.024 0.976
#> TCGA-06-0122-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0124-01A-01 3 0.5733 0.5125 0.000 0.324 0.676
#> TCGA-06-0130-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-06-0143-01A-01 3 0.1289 0.9220 0.000 0.032 0.968
#> TCGA-06-0147-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0152-01A-02 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0154-01A-02 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.3619 0.8469 0.000 0.864 0.136
#> TCGA-06-0189-01A-05 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-06-0210-01A-01 3 0.5988 0.3868 0.000 0.368 0.632
#> TCGA-06-0397-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-06-0409-01A-02 2 0.0592 0.9175 0.000 0.988 0.012
#> TCGA-06-0412-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-06-0645-01A-01 3 0.5948 0.3986 0.000 0.360 0.640
#> TCGA-08-0346-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-08-0352-01A-01 3 0.0000 0.9457 0.000 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-08-0392-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 2 0.4750 0.7552 0.000 0.784 0.216
#> TCGA-08-0512-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9223 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 2 0.6204 0.2432 0.000 0.576 0.424
#> TCGA-12-0620-01A-01 3 0.4702 0.7034 0.000 0.212 0.788
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 4 0.3649 0.7164 0.204 0.000 0.000 0.796
#> TCGA-02-0010-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0921 0.8857 0.972 0.000 0.028 0.000
#> TCGA-02-0047-01A-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-02-0048-01A-01 4 0.4981 0.1767 0.464 0.000 0.000 0.536
#> TCGA-02-0060-01A-01 4 0.3907 0.6751 0.232 0.000 0.000 0.768
#> TCGA-02-0069-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.3569 0.7388 0.804 0.000 0.196 0.000
#> TCGA-02-0084-01A-03 3 0.3024 0.8013 0.000 0.000 0.852 0.148
#> TCGA-02-0087-01A-01 1 0.4136 0.7293 0.788 0.000 0.196 0.016
#> TCGA-02-0104-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.4877 0.3472 0.592 0.000 0.408 0.000
#> TCGA-02-0325-01A-01 1 0.3569 0.7388 0.804 0.000 0.196 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.2216 0.8437 0.908 0.000 0.000 0.092
#> TCGA-02-0439-01A-01 1 0.3569 0.7505 0.804 0.000 0.000 0.196
#> TCGA-02-0440-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 4 0.2408 0.8118 0.104 0.000 0.000 0.896
#> TCGA-06-0128-01A-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0129-01A-01 1 0.2011 0.8449 0.920 0.000 0.000 0.080
#> TCGA-06-0146-01A-01 1 0.2216 0.8380 0.908 0.000 0.092 0.000
#> TCGA-06-0156-01A-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0166-01A-01 4 0.2408 0.8118 0.104 0.000 0.000 0.896
#> TCGA-06-0174-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.3569 0.7505 0.804 0.000 0.000 0.196
#> TCGA-06-0241-01A-02 1 0.4866 0.2364 0.596 0.000 0.000 0.404
#> TCGA-06-0410-01A-01 4 0.4855 0.2415 0.400 0.000 0.000 0.600
#> TCGA-06-0413-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.1716 0.8622 0.936 0.000 0.000 0.064
#> TCGA-06-0646-01A-01 3 0.2011 0.8670 0.000 0.000 0.920 0.080
#> TCGA-06-0648-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.1792 0.8585 0.932 0.000 0.000 0.068
#> TCGA-08-0344-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 4 0.6603 0.4180 0.104 0.000 0.316 0.580
#> TCGA-08-0348-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-08-0350-01A-01 1 0.3569 0.7388 0.804 0.000 0.196 0.000
#> TCGA-08-0353-01A-01 3 0.2011 0.8599 0.080 0.000 0.920 0.000
#> TCGA-08-0359-01A-01 1 0.5132 0.1368 0.548 0.000 0.004 0.448
#> TCGA-08-0385-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0469 0.8965 0.988 0.000 0.000 0.012
#> TCGA-08-0524-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 4 0.4957 0.4609 0.320 0.000 0.012 0.668
#> TCGA-12-0618-01A-01 1 0.0000 0.9022 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 4 0.1118 0.8591 0.000 0.000 0.036 0.964
#> TCGA-02-0113-01A-01 4 0.0336 0.8781 0.000 0.000 0.008 0.992
#> TCGA-02-0115-01A-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-02-0451-01A-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0132-01A-02 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0133-01A-02 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.3569 0.7505 0.804 0.000 0.000 0.196
#> TCGA-06-0162-01A-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.3688 0.7375 0.792 0.000 0.000 0.208
#> TCGA-06-0171-01A-02 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0179-01A-02 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 4 0.4431 0.5419 0.000 0.000 0.304 0.696
#> TCGA-06-0185-01A-01 4 0.4134 0.6182 0.000 0.000 0.260 0.740
#> TCGA-06-0195-01B-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0208-01B-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-08-0349-01A-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 4 0.4804 0.3444 0.000 0.384 0.000 0.616
#> TCGA-08-0386-01A-01 3 0.6301 0.5266 0.104 0.000 0.636 0.260
#> TCGA-08-0520-01A-01 4 0.0000 0.8827 0.000 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.1452 0.8948 0.036 0.000 0.956 0.008
#> TCGA-02-0009-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0016-01A-01 3 0.4643 0.4982 0.000 0.000 0.656 0.344
#> TCGA-02-0021-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0027-01A-01 3 0.2149 0.8599 0.000 0.000 0.912 0.088
#> TCGA-02-0038-01A-01 3 0.3569 0.7210 0.000 0.000 0.804 0.196
#> TCGA-02-0043-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0126-01A-01 3 0.3528 0.7499 0.000 0.000 0.808 0.192
#> TCGA-06-0137-01A-03 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-08-0354-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-08-0357-01A-01 3 0.3569 0.7448 0.000 0.000 0.804 0.196
#> TCGA-08-0358-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-08-0375-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-02-0057-01A-01 3 0.4477 0.5558 0.000 0.000 0.688 0.312
#> TCGA-02-0004-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.4605 0.5286 0.000 0.664 0.336 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.4843 0.4044 0.000 0.604 0.396 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.4543 0.5169 0.000 0.676 0.324 0.000
#> TCGA-02-0075-01A-01 2 0.0921 0.8774 0.000 0.972 0.028 0.000
#> TCGA-02-0079-01A-03 3 0.4500 0.5221 0.000 0.316 0.684 0.000
#> TCGA-02-0085-01A-01 4 0.6133 0.5789 0.000 0.188 0.136 0.676
#> TCGA-02-0086-01A-01 2 0.1118 0.8735 0.000 0.964 0.036 0.000
#> TCGA-02-0099-01A-01 2 0.4605 0.5286 0.000 0.664 0.336 0.000
#> TCGA-02-0106-01A-01 2 0.4992 0.0582 0.000 0.524 0.476 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0921 0.9033 0.028 0.000 0.972 0.000
#> TCGA-02-0337-01A-01 3 0.6468 0.3770 0.000 0.084 0.568 0.348
#> TCGA-06-0122-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0124-01A-01 3 0.4585 0.4725 0.000 0.332 0.668 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0154-01A-02 3 0.3486 0.7217 0.000 0.188 0.812 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.5489 0.4946 0.000 0.664 0.040 0.296
#> TCGA-06-0189-01A-05 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-06-0210-01A-01 3 0.4925 0.1623 0.000 0.428 0.572 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.2647 0.8062 0.000 0.880 0.120 0.000
#> TCGA-06-0412-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 3 0.2868 0.7977 0.000 0.136 0.864 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-08-0352-01A-01 3 0.0000 0.9217 0.000 0.000 1.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.3668 0.6874 0.000 0.808 0.004 0.188
#> TCGA-08-0392-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-08-0510-01A-01 2 0.4790 0.4393 0.000 0.620 0.380 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8969 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.4382 0.5500 0.000 0.704 0.296 0.000
#> TCGA-12-0620-01A-01 3 0.3123 0.7655 0.000 0.156 0.844 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 4 0.3857 0.5150 0.312 0.000 0.000 0.688 0.000
#> TCGA-02-0010-01A-01 1 0.4302 0.3342 0.520 0.000 0.000 0.000 0.480
#> TCGA-02-0011-01B-01 1 0.3684 0.4749 0.720 0.000 0.000 0.000 0.280
#> TCGA-02-0014-01A-01 1 0.2605 0.6189 0.852 0.000 0.000 0.000 0.148
#> TCGA-02-0024-01B-01 1 0.2605 0.6189 0.852 0.000 0.000 0.000 0.148
#> TCGA-02-0026-01B-01 1 0.4114 0.4467 0.624 0.000 0.000 0.000 0.376
#> TCGA-02-0028-01A-01 1 0.2690 0.6166 0.844 0.000 0.000 0.000 0.156
#> TCGA-02-0046-01A-01 1 0.0451 0.6363 0.988 0.000 0.008 0.000 0.004
#> TCGA-02-0047-01A-01 4 0.1544 0.8100 0.068 0.000 0.000 0.932 0.000
#> TCGA-02-0048-01A-01 1 0.4242 0.1780 0.572 0.000 0.000 0.428 0.000
#> TCGA-02-0060-01A-01 4 0.3074 0.6828 0.196 0.000 0.000 0.804 0.000
#> TCGA-02-0069-01A-01 1 0.4302 0.3342 0.520 0.000 0.000 0.000 0.480
#> TCGA-02-0074-01A-01 1 0.0000 0.6389 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.3949 0.4195 0.668 0.000 0.000 0.000 0.332
#> TCGA-02-0084-01A-03 5 0.6693 -0.1173 0.032 0.000 0.384 0.112 0.472
#> TCGA-02-0087-01A-01 1 0.4418 0.3969 0.652 0.000 0.000 0.016 0.332
#> TCGA-02-0104-01A-01 1 0.3074 0.5965 0.804 0.000 0.000 0.000 0.196
#> TCGA-02-0114-01A-01 1 0.2966 0.6043 0.816 0.000 0.000 0.000 0.184
#> TCGA-02-0281-01A-01 1 0.4138 0.4717 0.616 0.000 0.000 0.000 0.384
#> TCGA-02-0321-01A-01 1 0.4262 -0.0977 0.560 0.000 0.440 0.000 0.000
#> TCGA-02-0325-01A-01 1 0.3684 0.4749 0.720 0.000 0.000 0.000 0.280
#> TCGA-02-0338-01A-01 1 0.2605 0.6189 0.852 0.000 0.000 0.000 0.148
#> TCGA-02-0339-01A-01 1 0.4242 0.4168 0.572 0.000 0.000 0.000 0.428
#> TCGA-02-0432-01A-02 1 0.3949 0.4195 0.668 0.000 0.000 0.000 0.332
#> TCGA-02-0439-01A-01 1 0.3684 0.3845 0.720 0.000 0.000 0.280 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.6389 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 4 0.1544 0.8100 0.068 0.000 0.000 0.932 0.000
#> TCGA-06-0128-01A-01 4 0.1430 0.8208 0.004 0.000 0.000 0.944 0.052
#> TCGA-06-0129-01A-01 5 0.5507 -0.5730 0.456 0.000 0.000 0.064 0.480
#> TCGA-06-0146-01A-01 1 0.4302 0.3342 0.520 0.000 0.000 0.000 0.480
#> TCGA-06-0156-01A-01 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0166-01A-01 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0174-01A-01 1 0.0000 0.6389 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.2424 0.5942 0.868 0.000 0.000 0.000 0.132
#> TCGA-06-0238-01A-02 1 0.3684 0.3845 0.720 0.000 0.000 0.280 0.000
#> TCGA-06-0241-01A-02 1 0.3796 0.3460 0.700 0.000 0.000 0.300 0.000
#> TCGA-06-0410-01A-01 4 0.4210 0.1377 0.412 0.000 0.000 0.588 0.000
#> TCGA-06-0413-01A-01 1 0.2605 0.6189 0.852 0.000 0.000 0.000 0.148
#> TCGA-06-0414-01A-01 1 0.0404 0.6377 0.988 0.000 0.000 0.012 0.000
#> TCGA-06-0646-01A-01 3 0.1732 0.8085 0.000 0.000 0.920 0.080 0.000
#> TCGA-06-0648-01A-01 1 0.0000 0.6389 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.1965 0.6329 0.904 0.000 0.000 0.000 0.096
#> TCGA-08-0344-01A-01 1 0.1544 0.6377 0.932 0.000 0.000 0.000 0.068
#> TCGA-08-0347-01A-01 4 0.5406 0.2085 0.068 0.000 0.360 0.572 0.000
#> TCGA-08-0348-01A-01 1 0.0000 0.6389 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0350-01A-01 1 0.3949 0.4195 0.668 0.000 0.000 0.000 0.332
#> TCGA-08-0353-01A-01 3 0.3586 0.4978 0.264 0.000 0.736 0.000 0.000
#> TCGA-08-0359-01A-01 4 0.4430 0.3854 0.360 0.000 0.012 0.628 0.000
#> TCGA-08-0385-01A-01 1 0.3730 0.4828 0.712 0.000 0.000 0.000 0.288
#> TCGA-08-0517-01A-01 1 0.1792 0.6343 0.916 0.000 0.000 0.000 0.084
#> TCGA-08-0524-01A-01 1 0.2605 0.6189 0.852 0.000 0.000 0.000 0.148
#> TCGA-12-0616-01A-01 4 0.3391 0.6724 0.188 0.000 0.012 0.800 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.6389 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 4 0.3445 0.7223 0.000 0.000 0.036 0.824 0.140
#> TCGA-02-0113-01A-01 4 0.0290 0.8438 0.000 0.000 0.008 0.992 0.000
#> TCGA-02-0115-01A-01 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0451-01A-01 4 0.1197 0.8242 0.000 0.000 0.000 0.952 0.048
#> TCGA-06-0132-01A-02 4 0.1410 0.8160 0.000 0.000 0.000 0.940 0.060
#> TCGA-06-0133-01A-02 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0138-01A-02 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0160-01A-01 1 0.6706 0.1137 0.404 0.000 0.000 0.348 0.248
#> TCGA-06-0162-01A-01 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0167-01A-01 1 0.6706 0.1137 0.404 0.000 0.000 0.348 0.248
#> TCGA-06-0171-01A-02 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0173-01A-01 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0179-01A-02 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0182-01A-01 4 0.3816 0.4772 0.000 0.000 0.304 0.696 0.000
#> TCGA-06-0185-01A-01 4 0.3561 0.5489 0.000 0.000 0.260 0.740 0.000
#> TCGA-06-0195-01B-01 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0208-01B-01 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0214-01A-02 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0219-01A-01 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0221-01A-01 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0237-01A-02 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0240-01A-02 4 0.3480 0.6772 0.000 0.000 0.000 0.752 0.248
#> TCGA-08-0349-01A-01 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-08-0380-01A-01 4 0.4126 0.3288 0.000 0.380 0.000 0.620 0.000
#> TCGA-08-0386-01A-01 3 0.6645 -0.0407 0.292 0.000 0.448 0.260 0.000
#> TCGA-08-0520-01A-01 4 0.0000 0.8481 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0007-01A-01 3 0.1673 0.8311 0.032 0.000 0.944 0.008 0.016
#> TCGA-02-0009-01A-01 3 0.2424 0.8009 0.000 0.000 0.868 0.000 0.132
#> TCGA-02-0016-01A-01 3 0.5422 0.5322 0.000 0.000 0.656 0.212 0.132
#> TCGA-02-0021-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0027-01A-01 3 0.1851 0.8022 0.000 0.000 0.912 0.088 0.000
#> TCGA-02-0038-01A-01 3 0.3074 0.6208 0.000 0.000 0.804 0.196 0.000
#> TCGA-02-0043-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.2424 0.8009 0.000 0.000 0.868 0.000 0.132
#> TCGA-02-0269-01B-01 3 0.2424 0.8009 0.000 0.000 0.868 0.000 0.132
#> TCGA-02-0285-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0289-01A-01 3 0.2424 0.8009 0.000 0.000 0.868 0.000 0.132
#> TCGA-02-0290-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0317-01A-01 3 0.2424 0.8009 0.000 0.000 0.868 0.000 0.132
#> TCGA-02-0333-01A-02 3 0.2424 0.8009 0.000 0.000 0.868 0.000 0.132
#> TCGA-02-0422-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0162 0.8511 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0126-01A-01 3 0.3039 0.6851 0.000 0.000 0.808 0.192 0.000
#> TCGA-06-0137-01A-03 3 0.2377 0.8032 0.000 0.000 0.872 0.000 0.128
#> TCGA-06-0145-01A-04 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0354-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0357-01A-01 3 0.3074 0.6798 0.000 0.000 0.804 0.196 0.000
#> TCGA-08-0358-01A-01 3 0.2424 0.8009 0.000 0.000 0.868 0.000 0.132
#> TCGA-08-0375-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0518-01A-01 3 0.2179 0.8115 0.000 0.000 0.888 0.000 0.112
#> TCGA-08-0529-01A-02 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.2424 0.8009 0.000 0.000 0.868 0.000 0.132
#> TCGA-02-0057-01A-01 3 0.5258 0.5228 0.000 0.000 0.680 0.180 0.140
#> TCGA-02-0004-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.5444 0.6394 0.000 0.656 0.204 0.000 0.140
#> TCGA-02-0025-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.1270 0.8526 0.000 0.948 0.000 0.000 0.052
#> TCGA-02-0039-01A-01 2 0.2516 0.8338 0.000 0.860 0.000 0.000 0.140
#> TCGA-02-0051-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.4171 0.4249 0.000 0.604 0.396 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.5770 0.5164 0.000 0.604 0.256 0.000 0.140
#> TCGA-02-0075-01A-01 2 0.0794 0.8437 0.000 0.972 0.028 0.000 0.000
#> TCGA-02-0079-01A-03 3 0.5290 0.5189 0.000 0.184 0.676 0.000 0.140
#> TCGA-02-0085-01A-01 4 0.7425 0.3037 0.000 0.188 0.136 0.536 0.140
#> TCGA-02-0086-01A-01 2 0.2629 0.8345 0.000 0.860 0.004 0.000 0.136
#> TCGA-02-0099-01A-01 2 0.5240 0.6069 0.000 0.656 0.252 0.000 0.092
#> TCGA-02-0106-01A-01 2 0.4294 -0.0161 0.000 0.532 0.468 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.2516 0.8338 0.000 0.860 0.000 0.000 0.140
#> TCGA-02-0111-01A-01 2 0.2516 0.8338 0.000 0.860 0.000 0.000 0.140
#> TCGA-02-0326-01A-01 3 0.2583 0.7979 0.004 0.000 0.864 0.000 0.132
#> TCGA-02-0337-01A-01 3 0.7916 0.2102 0.032 0.080 0.508 0.240 0.140
#> TCGA-06-0122-01A-01 3 0.0609 0.8432 0.000 0.000 0.980 0.000 0.020
#> TCGA-06-0124-01A-01 3 0.5952 0.2542 0.000 0.324 0.548 0.000 0.128
#> TCGA-06-0130-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.2516 0.8338 0.000 0.860 0.000 0.000 0.140
#> TCGA-06-0143-01A-01 3 0.2516 0.7429 0.000 0.000 0.860 0.000 0.140
#> TCGA-06-0147-01A-01 2 0.2516 0.8338 0.000 0.860 0.000 0.000 0.140
#> TCGA-06-0149-01A-05 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0154-01A-02 3 0.3003 0.6494 0.000 0.188 0.812 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.2516 0.8338 0.000 0.860 0.000 0.000 0.140
#> TCGA-06-0175-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.6071 0.6451 0.000 0.656 0.040 0.164 0.140
#> TCGA-06-0189-01A-05 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.2280 0.8394 0.000 0.880 0.000 0.000 0.120
#> TCGA-06-0197-01A-02 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0210-01A-01 3 0.4497 0.1365 0.000 0.424 0.568 0.000 0.008
#> TCGA-06-0397-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.3011 0.8266 0.000 0.844 0.016 0.000 0.140
#> TCGA-06-0412-01A-01 3 0.0000 0.8520 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0645-01A-01 3 0.4764 0.5676 0.000 0.128 0.732 0.000 0.140
#> TCGA-08-0346-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0352-01A-01 3 0.2516 0.7429 0.000 0.000 0.860 0.000 0.140
#> TCGA-08-0360-01A-01 2 0.2516 0.8338 0.000 0.860 0.000 0.000 0.140
#> TCGA-08-0390-01A-01 2 0.3548 0.6681 0.000 0.796 0.004 0.188 0.012
#> TCGA-08-0392-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.2516 0.8338 0.000 0.860 0.000 0.000 0.140
#> TCGA-08-0510-01A-01 2 0.5470 0.5389 0.000 0.612 0.296 0.000 0.092
#> TCGA-08-0512-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8584 0.000 1.000 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.3774 0.4849 0.000 0.704 0.296 0.000 0.000
#> TCGA-12-0620-01A-01 3 0.2648 0.6973 0.000 0.152 0.848 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 6 0.3684 0.3800 0.372 0.000 0.000 0.000 0.000 0.628
#> TCGA-02-0010-01A-01 5 0.3409 0.6146 0.300 0.000 0.000 0.000 0.700 0.000
#> TCGA-02-0011-01B-01 1 0.3390 0.1660 0.704 0.000 0.000 0.000 0.296 0.000
#> TCGA-02-0014-01A-01 1 0.3330 0.3425 0.716 0.000 0.000 0.000 0.284 0.000
#> TCGA-02-0024-01B-01 1 0.3198 0.3640 0.740 0.000 0.000 0.000 0.260 0.000
#> TCGA-02-0026-01B-01 1 0.3868 -0.3424 0.504 0.000 0.000 0.000 0.496 0.000
#> TCGA-02-0028-01A-01 1 0.3409 0.3228 0.700 0.000 0.000 0.000 0.300 0.000
#> TCGA-02-0046-01A-01 1 0.0146 0.5384 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0047-01A-01 6 0.2823 0.6412 0.204 0.000 0.000 0.000 0.000 0.796
#> TCGA-02-0048-01A-01 1 0.3810 0.1516 0.572 0.000 0.000 0.000 0.000 0.428
#> TCGA-02-0060-01A-01 6 0.4868 0.3763 0.332 0.000 0.000 0.076 0.000 0.592
#> TCGA-02-0069-01A-01 5 0.3409 0.6146 0.300 0.000 0.000 0.000 0.700 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.5388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.3789 -0.0554 0.584 0.000 0.000 0.000 0.416 0.000
#> TCGA-02-0084-01A-03 5 0.5813 -0.0491 0.120 0.000 0.192 0.000 0.624 0.064
#> TCGA-02-0087-01A-01 1 0.4025 -0.0647 0.576 0.000 0.000 0.000 0.416 0.008
#> TCGA-02-0104-01A-01 1 0.3684 0.1900 0.628 0.000 0.000 0.000 0.372 0.000
#> TCGA-02-0114-01A-01 1 0.3634 0.2253 0.644 0.000 0.000 0.000 0.356 0.000
#> TCGA-02-0281-01A-01 5 0.3864 0.2487 0.480 0.000 0.000 0.000 0.520 0.000
#> TCGA-02-0321-01A-01 3 0.3854 0.1350 0.464 0.000 0.536 0.000 0.000 0.000
#> TCGA-02-0325-01A-01 1 0.3309 0.1901 0.720 0.000 0.000 0.000 0.280 0.000
#> TCGA-02-0338-01A-01 1 0.3330 0.3425 0.716 0.000 0.000 0.000 0.284 0.000
#> TCGA-02-0339-01A-01 5 0.3823 0.3680 0.436 0.000 0.000 0.000 0.564 0.000
#> TCGA-02-0432-01A-02 1 0.3789 -0.0554 0.584 0.000 0.000 0.000 0.416 0.000
#> TCGA-02-0439-01A-01 1 0.3309 0.2507 0.720 0.000 0.000 0.000 0.000 0.280
#> TCGA-02-0440-01A-01 1 0.0000 0.5388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 6 0.2854 0.6366 0.208 0.000 0.000 0.000 0.000 0.792
#> TCGA-06-0128-01A-01 6 0.2320 0.7089 0.004 0.000 0.000 0.000 0.132 0.864
#> TCGA-06-0129-01A-01 5 0.4181 0.5565 0.248 0.000 0.000 0.000 0.700 0.052
#> TCGA-06-0146-01A-01 5 0.3409 0.6146 0.300 0.000 0.000 0.000 0.700 0.000
#> TCGA-06-0156-01A-01 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0166-01A-01 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0174-01A-01 1 0.0000 0.5388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.2178 0.4214 0.868 0.000 0.000 0.000 0.132 0.000
#> TCGA-06-0238-01A-02 1 0.3309 0.2507 0.720 0.000 0.000 0.000 0.000 0.280
#> TCGA-06-0241-01A-02 1 0.2854 0.3738 0.792 0.000 0.000 0.000 0.000 0.208
#> TCGA-06-0410-01A-01 6 0.3782 0.1374 0.412 0.000 0.000 0.000 0.000 0.588
#> TCGA-06-0413-01A-01 1 0.3330 0.3425 0.716 0.000 0.000 0.000 0.284 0.000
#> TCGA-06-0414-01A-01 1 0.0146 0.5381 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-06-0646-01A-01 3 0.1556 0.8151 0.000 0.000 0.920 0.000 0.000 0.080
#> TCGA-06-0648-01A-01 1 0.0000 0.5388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.2219 0.4812 0.864 0.000 0.000 0.000 0.136 0.000
#> TCGA-08-0344-01A-01 1 0.2854 0.4021 0.792 0.000 0.000 0.000 0.208 0.000
#> TCGA-08-0347-01A-01 6 0.5807 0.1759 0.208 0.000 0.308 0.000 0.000 0.484
#> TCGA-08-0348-01A-01 1 0.0000 0.5388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-08-0350-01A-01 1 0.3789 -0.0554 0.584 0.000 0.000 0.000 0.416 0.000
#> TCGA-08-0353-01A-01 3 0.3221 0.5620 0.264 0.000 0.736 0.000 0.000 0.000
#> TCGA-08-0359-01A-01 6 0.3979 0.4250 0.360 0.000 0.012 0.000 0.000 0.628
#> TCGA-08-0385-01A-01 1 0.3499 0.1365 0.680 0.000 0.000 0.000 0.320 0.000
#> TCGA-08-0517-01A-01 1 0.1957 0.4964 0.888 0.000 0.000 0.000 0.112 0.000
#> TCGA-08-0524-01A-01 1 0.3330 0.3425 0.716 0.000 0.000 0.000 0.284 0.000
#> TCGA-12-0616-01A-01 6 0.2170 0.7359 0.100 0.000 0.012 0.000 0.000 0.888
#> TCGA-12-0618-01A-01 1 0.0000 0.5388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 6 0.3671 0.5860 0.000 0.000 0.036 0.000 0.208 0.756
#> TCGA-02-0113-01A-01 6 0.0260 0.8031 0.000 0.000 0.008 0.000 0.000 0.992
#> TCGA-02-0115-01A-01 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-02-0451-01A-01 6 0.1501 0.7597 0.000 0.000 0.000 0.000 0.076 0.924
#> TCGA-06-0132-01A-02 6 0.1714 0.7463 0.000 0.000 0.000 0.000 0.092 0.908
#> TCGA-06-0133-01A-02 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 4 0.1814 0.8911 0.100 0.000 0.000 0.900 0.000 0.000
#> TCGA-06-0162-01A-01 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 4 0.1814 0.8911 0.100 0.000 0.000 0.900 0.000 0.000
#> TCGA-06-0171-01A-02 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0179-01A-02 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 6 0.3428 0.4407 0.000 0.000 0.304 0.000 0.000 0.696
#> TCGA-06-0185-01A-01 6 0.3198 0.5119 0.000 0.000 0.260 0.000 0.000 0.740
#> TCGA-06-0195-01B-01 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0208-01B-01 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.1814 0.7978 0.000 0.000 0.000 0.900 0.000 0.100
#> TCGA-08-0349-01A-01 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 6 0.3830 0.2946 0.000 0.376 0.000 0.000 0.004 0.620
#> TCGA-08-0386-01A-01 3 0.5978 0.1041 0.296 0.000 0.444 0.000 0.000 0.260
#> TCGA-08-0520-01A-01 6 0.0000 0.8079 0.000 0.000 0.000 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.1862 0.8292 0.032 0.000 0.932 0.012 0.016 0.008
#> TCGA-02-0009-01A-01 3 0.3423 0.7756 0.000 0.000 0.812 0.100 0.088 0.000
#> TCGA-02-0016-01A-01 3 0.5672 0.6146 0.000 0.000 0.652 0.100 0.088 0.160
#> TCGA-02-0021-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0027-01A-01 3 0.1663 0.8101 0.000 0.000 0.912 0.000 0.000 0.088
#> TCGA-02-0038-01A-01 3 0.2762 0.6620 0.000 0.000 0.804 0.000 0.000 0.196
#> TCGA-02-0043-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.3423 0.7756 0.000 0.000 0.812 0.100 0.088 0.000
#> TCGA-02-0269-01B-01 3 0.3423 0.7756 0.000 0.000 0.812 0.100 0.088 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0289-01A-01 3 0.3423 0.7756 0.000 0.000 0.812 0.100 0.088 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0317-01A-01 3 0.3423 0.7756 0.000 0.000 0.812 0.100 0.088 0.000
#> TCGA-02-0333-01A-02 3 0.3423 0.7756 0.000 0.000 0.812 0.100 0.088 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0146 0.8458 0.000 0.000 0.996 0.000 0.004 0.000
#> TCGA-06-0126-01A-01 3 0.2730 0.7231 0.000 0.000 0.808 0.000 0.000 0.192
#> TCGA-06-0137-01A-03 3 0.3372 0.7780 0.000 0.000 0.816 0.100 0.084 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0402-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0354-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0357-01A-01 3 0.2762 0.7187 0.000 0.000 0.804 0.000 0.000 0.196
#> TCGA-08-0358-01A-01 3 0.3423 0.7756 0.000 0.000 0.812 0.100 0.088 0.000
#> TCGA-08-0375-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0518-01A-01 3 0.2856 0.7985 0.000 0.000 0.856 0.068 0.076 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.3423 0.7756 0.000 0.000 0.812 0.100 0.088 0.000
#> TCGA-02-0057-01A-01 3 0.4881 0.5751 0.000 0.000 0.656 0.000 0.208 0.136
#> TCGA-02-0004-01A-01 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.5374 0.5700 0.000 0.588 0.200 0.000 0.212 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.1863 0.7950 0.000 0.896 0.000 0.000 0.104 0.000
#> TCGA-02-0039-01A-01 2 0.2883 0.7693 0.000 0.788 0.000 0.000 0.212 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.3950 0.3530 0.000 0.564 0.432 0.000 0.004 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.5639 0.4601 0.000 0.536 0.252 0.000 0.212 0.000
#> TCGA-02-0075-01A-01 2 0.0858 0.7911 0.000 0.968 0.028 0.000 0.004 0.000
#> TCGA-02-0079-01A-03 3 0.5250 0.4923 0.000 0.184 0.608 0.000 0.208 0.000
#> TCGA-02-0085-01A-01 6 0.7053 0.1468 0.000 0.184 0.136 0.000 0.208 0.472
#> TCGA-02-0086-01A-01 2 0.2994 0.7700 0.000 0.788 0.004 0.000 0.208 0.000
#> TCGA-02-0099-01A-01 2 0.5188 0.5148 0.000 0.588 0.288 0.000 0.124 0.000
#> TCGA-02-0106-01A-01 2 0.3804 0.1134 0.000 0.576 0.424 0.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.2883 0.7693 0.000 0.788 0.000 0.000 0.212 0.000
#> TCGA-02-0111-01A-01 2 0.2883 0.7693 0.000 0.788 0.000 0.000 0.212 0.000
#> TCGA-02-0326-01A-01 3 0.3423 0.7756 0.000 0.000 0.812 0.100 0.088 0.000
#> TCGA-02-0337-01A-01 3 0.7884 0.1406 0.144 0.036 0.412 0.000 0.208 0.200
#> TCGA-06-0122-01A-01 3 0.0865 0.8325 0.000 0.000 0.964 0.000 0.036 0.000
#> TCGA-06-0124-01A-01 3 0.5552 0.3098 0.000 0.252 0.552 0.000 0.196 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.2883 0.7693 0.000 0.788 0.000 0.000 0.212 0.000
#> TCGA-06-0143-01A-01 3 0.2854 0.6923 0.000 0.000 0.792 0.000 0.208 0.000
#> TCGA-06-0147-01A-01 2 0.2883 0.7693 0.000 0.788 0.000 0.000 0.212 0.000
#> TCGA-06-0149-01A-05 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0154-01A-02 3 0.2491 0.7082 0.000 0.164 0.836 0.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.2883 0.7693 0.000 0.788 0.000 0.000 0.212 0.000
#> TCGA-06-0175-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.5933 0.5599 0.000 0.588 0.040 0.000 0.212 0.160
#> TCGA-06-0189-01A-05 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0458 0.8060 0.000 0.984 0.000 0.000 0.016 0.000
#> TCGA-06-0194-01A-01 2 0.2697 0.7769 0.000 0.812 0.000 0.000 0.188 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0210-01A-01 3 0.3984 0.2023 0.000 0.396 0.596 0.000 0.008 0.000
#> TCGA-06-0397-01A-01 2 0.0146 0.8054 0.000 0.996 0.000 0.000 0.004 0.000
#> TCGA-06-0409-01A-02 2 0.3230 0.7633 0.000 0.776 0.012 0.000 0.212 0.000
#> TCGA-06-0412-01A-01 3 0.0000 0.8465 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0645-01A-01 3 0.4251 0.6028 0.000 0.076 0.716 0.000 0.208 0.000
#> TCGA-08-0346-01A-01 2 0.0547 0.8058 0.000 0.980 0.000 0.000 0.020 0.000
#> TCGA-08-0352-01A-01 3 0.2854 0.6923 0.000 0.000 0.792 0.000 0.208 0.000
#> TCGA-08-0360-01A-01 2 0.2883 0.7693 0.000 0.788 0.000 0.000 0.212 0.000
#> TCGA-08-0390-01A-01 2 0.3316 0.6250 0.000 0.804 0.004 0.000 0.028 0.164
#> TCGA-08-0392-01A-01 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.2883 0.7693 0.000 0.788 0.000 0.000 0.212 0.000
#> TCGA-08-0510-01A-01 2 0.5378 0.4572 0.000 0.544 0.324 0.000 0.132 0.000
#> TCGA-08-0512-01A-01 2 0.0146 0.8054 0.000 0.996 0.000 0.000 0.004 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8056 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.3409 0.4274 0.000 0.700 0.300 0.000 0.000 0.000
#> TCGA-12-0620-01A-01 3 0.2631 0.7135 0.000 0.152 0.840 0.000 0.008 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> MAD:pam 169 1.80e-27 2
#> MAD:pam 163 1.65e-38 3
#> MAD:pam 157 8.88e-59 4
#> MAD:pam 137 1.90e-54 5
#> MAD:pam 127 1.60e-45 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "mclust"]
# you can also extract it by
# res = res_list["MAD:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.872 0.917 0.966 0.4969 0.502 0.502
#> 3 3 0.472 0.648 0.767 0.2599 0.792 0.603
#> 4 4 0.719 0.774 0.883 0.1812 0.849 0.590
#> 5 5 0.777 0.833 0.890 0.0537 0.893 0.629
#> 6 6 0.760 0.720 0.853 0.0361 0.935 0.731
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0048-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.5294 0.8537 0.880 0.120
#> TCGA-02-0084-01A-03 1 0.7056 0.7665 0.808 0.192
#> TCGA-02-0087-01A-01 1 0.5294 0.8537 0.880 0.120
#> TCGA-02-0104-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.2778 0.9202 0.952 0.048
#> TCGA-02-0325-01A-01 1 0.5842 0.8318 0.860 0.140
#> TCGA-02-0338-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.5059 0.8621 0.888 0.112
#> TCGA-02-0440-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0128-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0166-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0174-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0646-01A-01 1 0.5059 0.8621 0.888 0.112
#> TCGA-06-0648-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.3114 0.9136 0.944 0.056
#> TCGA-08-0348-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.0672 0.9509 0.992 0.008
#> TCGA-08-0353-01A-01 2 0.9710 0.3385 0.400 0.600
#> TCGA-08-0359-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0089-01A-01 1 0.9732 0.3645 0.596 0.404
#> TCGA-02-0113-01A-01 2 0.4298 0.8831 0.088 0.912
#> TCGA-02-0115-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-02-0451-01A-01 1 0.0376 0.9538 0.996 0.004
#> TCGA-06-0132-01A-02 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0133-01A-02 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0138-01A-02 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0160-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0162-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0167-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0171-01A-02 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0173-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0179-01A-02 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0182-01A-01 2 0.9710 0.3385 0.400 0.600
#> TCGA-06-0185-01A-01 2 0.9686 0.3487 0.396 0.604
#> TCGA-06-0195-01B-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0208-01B-01 1 0.9710 0.3345 0.600 0.400
#> TCGA-06-0214-01A-02 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0219-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0221-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0237-01A-02 1 0.0000 0.9565 1.000 0.000
#> TCGA-06-0240-01A-02 1 0.0000 0.9565 1.000 0.000
#> TCGA-08-0349-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-08-0380-01A-01 1 0.0000 0.9565 1.000 0.000
#> TCGA-08-0386-01A-01 1 0.8443 0.6278 0.728 0.272
#> TCGA-08-0520-01A-01 1 0.9323 0.4694 0.652 0.348
#> TCGA-02-0007-01A-01 1 0.7815 0.6952 0.768 0.232
#> TCGA-02-0009-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0016-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0021-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0023-01B-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0027-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0038-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0043-01A-01 2 0.0672 0.9652 0.008 0.992
#> TCGA-02-0070-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0102-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0260-01A-03 2 0.0672 0.9652 0.008 0.992
#> TCGA-02-0269-01B-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0285-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0289-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0290-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0317-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0333-01A-02 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0422-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0430-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-06-0125-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-06-0126-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-06-0137-01A-03 2 0.0376 0.9684 0.004 0.996
#> TCGA-06-0145-01A-04 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0148-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-06-0187-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0211-01B-01 2 0.8144 0.6600 0.252 0.748
#> TCGA-06-0402-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-08-0246-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-08-0357-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-08-0358-01A-01 2 0.8386 0.6193 0.268 0.732
#> TCGA-08-0375-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-08-0511-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-08-0514-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-08-0529-01A-02 2 0.0376 0.9684 0.004 0.996
#> TCGA-08-0531-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0057-01A-01 1 0.9922 0.2324 0.552 0.448
#> TCGA-02-0004-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0376 0.9684 0.004 0.996
#> TCGA-02-0085-01A-01 1 0.6438 0.8033 0.836 0.164
#> TCGA-02-0086-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.9977 0.0463 0.472 0.528
#> TCGA-02-0337-01A-01 2 0.8909 0.5296 0.308 0.692
#> TCGA-06-0122-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.0376 0.9684 0.004 0.996
#> TCGA-06-0147-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0376 0.9684 0.004 0.996
#> TCGA-06-0154-01A-02 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9693 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9693 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.9693 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.2903 0.8280 0.924 0.048 0.028
#> TCGA-02-0010-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.5524 0.7538 0.796 0.164 0.040
#> TCGA-02-0014-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.4195 0.8066 0.852 0.012 0.136
#> TCGA-02-0047-01A-01 1 0.3879 0.7989 0.848 0.000 0.152
#> TCGA-02-0048-01A-01 3 0.9110 -0.1454 0.420 0.140 0.440
#> TCGA-02-0060-01A-01 1 0.3083 0.8345 0.916 0.024 0.060
#> TCGA-02-0069-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.6521 0.6876 0.712 0.248 0.040
#> TCGA-02-0084-01A-03 1 0.5529 0.6648 0.704 0.000 0.296
#> TCGA-02-0087-01A-01 1 0.6062 0.7832 0.780 0.072 0.148
#> TCGA-02-0104-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.6090 0.6929 0.716 0.020 0.264
#> TCGA-02-0325-01A-01 1 0.6976 0.7039 0.700 0.064 0.236
#> TCGA-02-0338-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.6521 0.6876 0.712 0.248 0.040
#> TCGA-02-0439-01A-01 1 0.7739 0.7145 0.672 0.124 0.204
#> TCGA-02-0440-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.3879 0.7989 0.848 0.000 0.152
#> TCGA-06-0128-01A-01 1 0.1529 0.8382 0.960 0.000 0.040
#> TCGA-06-0129-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.1620 0.8387 0.964 0.024 0.012
#> TCGA-06-0156-01A-01 1 0.3879 0.7989 0.848 0.000 0.152
#> TCGA-06-0166-01A-01 1 0.3879 0.7989 0.848 0.000 0.152
#> TCGA-06-0174-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0592 0.8433 0.988 0.000 0.012
#> TCGA-06-0238-01A-02 1 0.1647 0.8396 0.960 0.004 0.036
#> TCGA-06-0241-01A-02 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0592 0.8433 0.988 0.000 0.012
#> TCGA-06-0413-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 1 0.7918 0.6454 0.660 0.136 0.204
#> TCGA-06-0648-01A-01 1 0.0592 0.8433 0.988 0.000 0.012
#> TCGA-08-0245-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-08-0347-01A-01 1 0.3879 0.7989 0.848 0.000 0.152
#> TCGA-08-0348-01A-01 1 0.2356 0.8314 0.928 0.000 0.072
#> TCGA-08-0350-01A-01 1 0.1289 0.8416 0.968 0.000 0.032
#> TCGA-08-0353-01A-01 3 0.7606 0.3688 0.244 0.092 0.664
#> TCGA-08-0359-01A-01 1 0.2796 0.8244 0.908 0.000 0.092
#> TCGA-08-0385-01A-01 1 0.0592 0.8433 0.988 0.000 0.012
#> TCGA-08-0517-01A-01 1 0.0424 0.8433 0.992 0.000 0.008
#> TCGA-08-0524-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0592 0.8433 0.988 0.000 0.012
#> TCGA-12-0618-01A-01 1 0.0000 0.8430 1.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.9885 -0.0917 0.308 0.408 0.284
#> TCGA-02-0113-01A-01 3 0.6388 0.3792 0.284 0.024 0.692
#> TCGA-02-0115-01A-01 1 0.9941 0.0976 0.376 0.340 0.284
#> TCGA-02-0451-01A-01 1 0.9842 0.0859 0.384 0.248 0.368
#> TCGA-06-0132-01A-02 1 0.5517 0.6949 0.728 0.004 0.268
#> TCGA-06-0133-01A-02 1 0.9243 0.3746 0.492 0.168 0.340
#> TCGA-06-0138-01A-02 1 0.8771 0.4435 0.544 0.132 0.324
#> TCGA-06-0160-01A-01 1 0.6559 0.6860 0.708 0.252 0.040
#> TCGA-06-0162-01A-01 1 0.7848 0.6093 0.640 0.096 0.264
#> TCGA-06-0167-01A-01 1 0.6559 0.6860 0.708 0.252 0.040
#> TCGA-06-0171-01A-02 1 0.5167 0.7773 0.804 0.024 0.172
#> TCGA-06-0173-01A-01 1 0.8821 0.3953 0.524 0.128 0.348
#> TCGA-06-0179-01A-02 1 0.5517 0.6946 0.728 0.004 0.268
#> TCGA-06-0182-01A-01 3 0.6228 0.1879 0.372 0.004 0.624
#> TCGA-06-0185-01A-01 3 0.6008 0.1814 0.372 0.000 0.628
#> TCGA-06-0195-01B-01 1 0.1765 0.8385 0.956 0.004 0.040
#> TCGA-06-0208-01B-01 3 0.7395 0.1134 0.380 0.040 0.580
#> TCGA-06-0214-01A-02 1 0.8913 0.3614 0.508 0.132 0.360
#> TCGA-06-0219-01A-01 1 0.4514 0.7936 0.832 0.012 0.156
#> TCGA-06-0221-01A-01 1 0.1765 0.8385 0.956 0.004 0.040
#> TCGA-06-0237-01A-02 1 0.8872 0.3897 0.520 0.132 0.348
#> TCGA-06-0240-01A-02 1 0.6559 0.6860 0.708 0.252 0.040
#> TCGA-08-0349-01A-01 1 0.8659 0.4773 0.560 0.128 0.312
#> TCGA-08-0380-01A-01 1 0.9594 0.2139 0.436 0.204 0.360
#> TCGA-08-0386-01A-01 3 0.6026 0.1708 0.376 0.000 0.624
#> TCGA-08-0520-01A-01 3 0.6598 -0.0159 0.428 0.008 0.564
#> TCGA-02-0007-01A-01 3 0.6267 -0.0968 0.452 0.000 0.548
#> TCGA-02-0009-01A-01 3 0.0892 0.6558 0.000 0.020 0.980
#> TCGA-02-0016-01A-01 3 0.0424 0.6566 0.000 0.008 0.992
#> TCGA-02-0021-01A-01 3 0.2066 0.6416 0.000 0.060 0.940
#> TCGA-02-0023-01B-01 3 0.1289 0.6496 0.000 0.032 0.968
#> TCGA-02-0027-01A-01 3 0.3607 0.6124 0.112 0.008 0.880
#> TCGA-02-0038-01A-01 3 0.4291 0.5180 0.000 0.180 0.820
#> TCGA-02-0043-01A-01 3 0.4978 0.6003 0.004 0.216 0.780
#> TCGA-02-0070-01A-01 3 0.3551 0.5713 0.000 0.132 0.868
#> TCGA-02-0102-01A-01 3 0.2066 0.6416 0.000 0.060 0.940
#> TCGA-02-0260-01A-03 3 0.3941 0.5897 0.000 0.156 0.844
#> TCGA-02-0269-01B-01 3 0.0000 0.6572 0.000 0.000 1.000
#> TCGA-02-0285-01A-01 3 0.3619 0.5661 0.000 0.136 0.864
#> TCGA-02-0289-01A-01 3 0.0747 0.6563 0.000 0.016 0.984
#> TCGA-02-0290-01A-01 3 0.3941 0.5451 0.000 0.156 0.844
#> TCGA-02-0317-01A-01 3 0.0000 0.6572 0.000 0.000 1.000
#> TCGA-02-0333-01A-02 3 0.0000 0.6572 0.000 0.000 1.000
#> TCGA-02-0422-01A-01 3 0.2165 0.6393 0.000 0.064 0.936
#> TCGA-02-0430-01A-01 3 0.2066 0.6416 0.000 0.060 0.940
#> TCGA-06-0125-01A-01 3 0.0237 0.6572 0.000 0.004 0.996
#> TCGA-06-0126-01A-01 3 0.0000 0.6572 0.000 0.000 1.000
#> TCGA-06-0137-01A-03 3 0.0000 0.6572 0.000 0.000 1.000
#> TCGA-06-0145-01A-04 3 0.3941 0.5374 0.000 0.156 0.844
#> TCGA-06-0148-01A-01 3 0.3619 0.5841 0.000 0.136 0.864
#> TCGA-06-0187-01A-01 3 0.4346 0.4981 0.000 0.184 0.816
#> TCGA-06-0211-01B-01 3 0.7287 0.4254 0.212 0.092 0.696
#> TCGA-06-0402-01A-01 3 0.2537 0.6291 0.000 0.080 0.920
#> TCGA-08-0246-01A-01 3 0.4887 0.4181 0.000 0.228 0.772
#> TCGA-08-0354-01A-01 3 0.4796 0.4364 0.000 0.220 0.780
#> TCGA-08-0355-01A-01 3 0.2537 0.6254 0.000 0.080 0.920
#> TCGA-08-0357-01A-01 3 0.0829 0.6567 0.012 0.004 0.984
#> TCGA-08-0358-01A-01 3 0.6243 0.5681 0.124 0.100 0.776
#> TCGA-08-0375-01A-01 3 0.3482 0.6052 0.000 0.128 0.872
#> TCGA-08-0511-01A-01 3 0.3816 0.5482 0.000 0.148 0.852
#> TCGA-08-0514-01A-01 3 0.3941 0.5384 0.000 0.156 0.844
#> TCGA-08-0518-01A-01 3 0.2796 0.6193 0.000 0.092 0.908
#> TCGA-08-0529-01A-02 3 0.2796 0.6193 0.000 0.092 0.908
#> TCGA-08-0531-01A-01 3 0.2537 0.6305 0.000 0.080 0.920
#> TCGA-02-0057-01A-01 3 0.9379 0.1479 0.180 0.348 0.472
#> TCGA-02-0004-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-02-0006-01B-01 2 0.5988 0.7942 0.000 0.632 0.368
#> TCGA-02-0025-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-02-0033-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-02-0034-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-02-0039-01A-01 2 0.5948 0.8116 0.000 0.640 0.360
#> TCGA-02-0051-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-02-0054-01A-01 2 0.5948 0.8071 0.000 0.640 0.360
#> TCGA-02-0055-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-02-0059-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-02-0064-01A-01 2 0.5465 0.8352 0.000 0.712 0.288
#> TCGA-02-0075-01A-01 2 0.5859 0.8279 0.000 0.656 0.344
#> TCGA-02-0079-01A-03 2 0.5859 0.8238 0.000 0.656 0.344
#> TCGA-02-0085-01A-01 1 0.6168 0.7377 0.740 0.036 0.224
#> TCGA-02-0086-01A-01 2 0.5650 0.8550 0.000 0.688 0.312
#> TCGA-02-0099-01A-01 2 0.5926 0.8115 0.000 0.644 0.356
#> TCGA-02-0106-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-02-0107-01A-01 2 0.5733 0.8471 0.000 0.676 0.324
#> TCGA-02-0111-01A-01 2 0.5178 0.8899 0.000 0.744 0.256
#> TCGA-02-0326-01A-01 3 0.5706 0.3216 0.320 0.000 0.680
#> TCGA-02-0337-01A-01 2 0.9278 0.5321 0.196 0.516 0.288
#> TCGA-06-0122-01A-01 3 0.6309 -0.5474 0.000 0.500 0.500
#> TCGA-06-0124-01A-01 2 0.5948 0.7743 0.000 0.640 0.360
#> TCGA-06-0130-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-06-0139-01A-01 2 0.5178 0.8899 0.000 0.744 0.256
#> TCGA-06-0143-01A-01 2 0.6302 0.5991 0.000 0.520 0.480
#> TCGA-06-0147-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-06-0149-01A-05 3 0.6309 -0.5474 0.000 0.500 0.500
#> TCGA-06-0152-01A-02 3 0.5111 0.5367 0.024 0.168 0.808
#> TCGA-06-0154-01A-02 2 0.6079 0.7719 0.000 0.612 0.388
#> TCGA-06-0164-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-06-0175-01A-01 3 0.6140 -0.2343 0.000 0.404 0.596
#> TCGA-06-0176-01A-03 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-06-0184-01A-01 2 0.6026 0.7881 0.000 0.624 0.376
#> TCGA-06-0189-01A-05 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-06-0190-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-06-0194-01A-01 2 0.5178 0.8899 0.000 0.744 0.256
#> TCGA-06-0197-01A-02 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-06-0210-01A-01 2 0.6225 0.7008 0.000 0.568 0.432
#> TCGA-06-0397-01A-01 2 0.5254 0.8861 0.000 0.736 0.264
#> TCGA-06-0409-01A-02 2 0.5733 0.8468 0.000 0.676 0.324
#> TCGA-06-0412-01A-01 3 0.6309 -0.5404 0.000 0.496 0.504
#> TCGA-06-0644-01A-02 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-06-0645-01A-01 2 0.5760 0.8438 0.000 0.672 0.328
#> TCGA-08-0346-01A-01 2 0.5810 0.8416 0.000 0.664 0.336
#> TCGA-08-0352-01A-01 3 0.6309 -0.5474 0.000 0.500 0.500
#> TCGA-08-0360-01A-01 2 0.5178 0.8899 0.000 0.744 0.256
#> TCGA-08-0390-01A-01 2 0.5835 0.8213 0.000 0.660 0.340
#> TCGA-08-0392-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-08-0509-01A-01 2 0.5760 0.8438 0.000 0.672 0.328
#> TCGA-08-0510-01A-01 2 0.6308 0.5558 0.000 0.508 0.492
#> TCGA-08-0512-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-08-0522-01A-01 2 0.5138 0.8904 0.000 0.748 0.252
#> TCGA-12-0619-01A-01 2 0.5178 0.8899 0.000 0.744 0.256
#> TCGA-12-0620-01A-01 3 0.6302 -0.4895 0.000 0.480 0.520
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.4222 0.6429 0.728 0.000 0.000 0.272
#> TCGA-02-0010-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.4250 0.6380 0.724 0.000 0.000 0.276
#> TCGA-02-0014-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 4 0.4018 0.6569 0.224 0.000 0.004 0.772
#> TCGA-02-0047-01A-01 4 0.1792 0.7997 0.068 0.000 0.000 0.932
#> TCGA-02-0048-01A-01 4 0.4567 0.5802 0.276 0.000 0.008 0.716
#> TCGA-02-0060-01A-01 1 0.6147 0.3903 0.564 0.000 0.056 0.380
#> TCGA-02-0069-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.6495 0.4905 0.608 0.000 0.108 0.284
#> TCGA-02-0084-01A-03 4 0.5218 0.7297 0.064 0.000 0.200 0.736
#> TCGA-02-0087-01A-01 4 0.7336 0.5172 0.284 0.000 0.196 0.520
#> TCGA-02-0104-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 4 0.5911 0.7214 0.112 0.000 0.196 0.692
#> TCGA-02-0325-01A-01 4 0.7271 0.5249 0.276 0.000 0.192 0.532
#> TCGA-02-0338-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.5549 0.5876 0.672 0.000 0.048 0.280
#> TCGA-02-0439-01A-01 4 0.3751 0.7092 0.004 0.000 0.196 0.800
#> TCGA-02-0440-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 4 0.4584 0.5338 0.300 0.004 0.000 0.696
#> TCGA-06-0128-01A-01 1 0.4746 0.4760 0.632 0.000 0.000 0.368
#> TCGA-06-0129-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.1975 0.8322 0.936 0.000 0.016 0.048
#> TCGA-06-0156-01A-01 4 0.4514 0.7871 0.112 0.004 0.072 0.812
#> TCGA-06-0166-01A-01 4 0.5247 0.7755 0.112 0.004 0.120 0.764
#> TCGA-06-0174-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-06-0238-01A-02 1 0.3400 0.7317 0.820 0.000 0.000 0.180
#> TCGA-06-0241-01A-02 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 4 0.5525 0.7335 0.076 0.004 0.192 0.728
#> TCGA-06-0648-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0336 0.8663 0.992 0.000 0.000 0.008
#> TCGA-08-0347-01A-01 4 0.5250 0.7327 0.068 0.000 0.196 0.736
#> TCGA-08-0348-01A-01 1 0.5883 0.5668 0.700 0.000 0.128 0.172
#> TCGA-08-0350-01A-01 1 0.2216 0.7950 0.908 0.000 0.092 0.000
#> TCGA-08-0353-01A-01 3 0.4049 0.6927 0.008 0.000 0.780 0.212
#> TCGA-08-0359-01A-01 4 0.4905 0.3426 0.364 0.000 0.004 0.632
#> TCGA-08-0385-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.8705 1.000 0.000 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.0336 0.8663 0.992 0.000 0.000 0.008
#> TCGA-02-0089-01A-01 4 0.6106 0.2478 0.000 0.060 0.348 0.592
#> TCGA-02-0113-01A-01 3 0.5309 0.6125 0.004 0.028 0.688 0.280
#> TCGA-02-0115-01A-01 4 0.4044 0.6915 0.004 0.024 0.152 0.820
#> TCGA-02-0451-01A-01 4 0.2586 0.8003 0.068 0.008 0.012 0.912
#> TCGA-06-0132-01A-02 4 0.1792 0.7997 0.068 0.000 0.000 0.932
#> TCGA-06-0133-01A-02 4 0.0188 0.7825 0.004 0.000 0.000 0.996
#> TCGA-06-0138-01A-02 4 0.1792 0.7997 0.068 0.000 0.000 0.932
#> TCGA-06-0160-01A-01 1 0.4994 0.3438 0.520 0.000 0.000 0.480
#> TCGA-06-0162-01A-01 4 0.1792 0.7997 0.068 0.000 0.000 0.932
#> TCGA-06-0167-01A-01 1 0.4994 0.3438 0.520 0.000 0.000 0.480
#> TCGA-06-0171-01A-02 4 0.1792 0.7997 0.068 0.000 0.000 0.932
#> TCGA-06-0173-01A-01 4 0.2561 0.8036 0.068 0.004 0.016 0.912
#> TCGA-06-0179-01A-02 4 0.1792 0.7997 0.068 0.000 0.000 0.932
#> TCGA-06-0182-01A-01 3 0.5497 0.3460 0.008 0.008 0.572 0.412
#> TCGA-06-0185-01A-01 3 0.5201 0.4149 0.004 0.004 0.592 0.400
#> TCGA-06-0195-01B-01 1 0.4843 0.4283 0.604 0.000 0.000 0.396
#> TCGA-06-0208-01B-01 4 0.2714 0.7397 0.004 0.000 0.112 0.884
#> TCGA-06-0214-01A-02 4 0.1978 0.7999 0.068 0.004 0.000 0.928
#> TCGA-06-0219-01A-01 4 0.2530 0.7768 0.112 0.000 0.000 0.888
#> TCGA-06-0221-01A-01 1 0.4356 0.6089 0.708 0.000 0.000 0.292
#> TCGA-06-0237-01A-02 4 0.0188 0.7825 0.004 0.000 0.000 0.996
#> TCGA-06-0240-01A-02 1 0.4994 0.3438 0.520 0.000 0.000 0.480
#> TCGA-08-0349-01A-01 4 0.1716 0.7996 0.064 0.000 0.000 0.936
#> TCGA-08-0380-01A-01 4 0.1792 0.7997 0.068 0.000 0.000 0.932
#> TCGA-08-0386-01A-01 4 0.3933 0.7044 0.008 0.000 0.200 0.792
#> TCGA-08-0520-01A-01 4 0.1209 0.7841 0.004 0.000 0.032 0.964
#> TCGA-02-0007-01A-01 4 0.4706 0.6697 0.020 0.000 0.248 0.732
#> TCGA-02-0009-01A-01 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-02-0016-01A-01 3 0.0592 0.8721 0.000 0.000 0.984 0.016
#> TCGA-02-0021-01A-01 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-02-0023-01B-01 3 0.0469 0.8735 0.000 0.000 0.988 0.012
#> TCGA-02-0027-01A-01 3 0.4843 0.3072 0.000 0.000 0.604 0.396
#> TCGA-02-0038-01A-01 3 0.4389 0.7752 0.000 0.072 0.812 0.116
#> TCGA-02-0043-01A-01 3 0.1978 0.8452 0.004 0.000 0.928 0.068
#> TCGA-02-0070-01A-01 3 0.1792 0.8456 0.000 0.000 0.932 0.068
#> TCGA-02-0102-01A-01 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 3 0.2124 0.8440 0.000 0.008 0.924 0.068
#> TCGA-02-0289-01A-01 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.2198 0.8410 0.000 0.008 0.920 0.072
#> TCGA-02-0317-01A-01 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 3 0.0188 0.8752 0.000 0.004 0.996 0.000
#> TCGA-02-0430-01A-01 3 0.0188 0.8756 0.000 0.000 0.996 0.004
#> TCGA-06-0125-01A-01 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-06-0137-01A-03 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-06-0145-01A-04 3 0.0188 0.8752 0.000 0.004 0.996 0.000
#> TCGA-06-0148-01A-01 3 0.1792 0.8456 0.000 0.000 0.932 0.068
#> TCGA-06-0187-01A-01 3 0.1209 0.8595 0.000 0.032 0.964 0.004
#> TCGA-06-0211-01B-01 3 0.4011 0.6976 0.008 0.000 0.784 0.208
#> TCGA-06-0402-01A-01 3 0.1978 0.8450 0.000 0.004 0.928 0.068
#> TCGA-08-0246-01A-01 3 0.3280 0.7801 0.000 0.124 0.860 0.016
#> TCGA-08-0354-01A-01 3 0.5247 0.7008 0.000 0.148 0.752 0.100
#> TCGA-08-0355-01A-01 3 0.1302 0.8612 0.000 0.000 0.956 0.044
#> TCGA-08-0357-01A-01 3 0.0469 0.8735 0.000 0.000 0.988 0.012
#> TCGA-08-0358-01A-01 3 0.4098 0.6995 0.012 0.000 0.784 0.204
#> TCGA-08-0375-01A-01 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-08-0511-01A-01 3 0.0188 0.8752 0.000 0.004 0.996 0.000
#> TCGA-08-0514-01A-01 3 0.0188 0.8752 0.000 0.004 0.996 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-08-0529-01A-02 3 0.0188 0.8752 0.000 0.004 0.996 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.8756 0.000 0.000 1.000 0.000
#> TCGA-02-0057-01A-01 4 0.5821 0.2283 0.000 0.032 0.432 0.536
#> TCGA-02-0004-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.3760 0.8077 0.000 0.836 0.028 0.136
#> TCGA-02-0025-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.2563 0.8762 0.000 0.908 0.020 0.072
#> TCGA-02-0051-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.3557 0.8354 0.000 0.856 0.036 0.108
#> TCGA-02-0055-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.0707 0.9113 0.000 0.980 0.020 0.000
#> TCGA-02-0075-01A-01 2 0.0895 0.9118 0.000 0.976 0.020 0.004
#> TCGA-02-0079-01A-03 2 0.2670 0.8743 0.000 0.904 0.024 0.072
#> TCGA-02-0085-01A-01 4 0.2965 0.7940 0.072 0.036 0.000 0.892
#> TCGA-02-0086-01A-01 2 0.0469 0.9161 0.000 0.988 0.012 0.000
#> TCGA-02-0099-01A-01 2 0.3182 0.8526 0.000 0.876 0.028 0.096
#> TCGA-02-0106-01A-01 2 0.0336 0.9161 0.000 0.992 0.008 0.000
#> TCGA-02-0107-01A-01 2 0.2053 0.8816 0.000 0.924 0.004 0.072
#> TCGA-02-0111-01A-01 2 0.0188 0.9177 0.000 0.996 0.004 0.000
#> TCGA-02-0326-01A-01 4 0.5257 0.7197 0.060 0.000 0.212 0.728
#> TCGA-02-0337-01A-01 4 0.5543 0.3459 0.000 0.360 0.028 0.612
#> TCGA-06-0122-01A-01 2 0.6215 0.4332 0.000 0.600 0.328 0.072
#> TCGA-06-0124-01A-01 2 0.2413 0.8845 0.000 0.916 0.020 0.064
#> TCGA-06-0130-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0188 0.9177 0.000 0.996 0.004 0.000
#> TCGA-06-0143-01A-01 2 0.6141 0.4810 0.000 0.616 0.312 0.072
#> TCGA-06-0147-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.6396 0.3425 0.000 0.360 0.564 0.076
#> TCGA-06-0152-01A-02 3 0.3591 0.7458 0.000 0.008 0.824 0.168
#> TCGA-06-0154-01A-02 2 0.0707 0.9113 0.000 0.980 0.020 0.000
#> TCGA-06-0164-01A-01 2 0.0188 0.9177 0.000 0.996 0.004 0.000
#> TCGA-06-0175-01A-01 2 0.7271 0.3534 0.000 0.532 0.276 0.192
#> TCGA-06-0176-01A-03 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.4869 0.7619 0.000 0.780 0.088 0.132
#> TCGA-06-0189-01A-05 2 0.0188 0.9177 0.000 0.996 0.004 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0188 0.9177 0.000 0.996 0.004 0.000
#> TCGA-06-0197-01A-02 2 0.0188 0.9177 0.000 0.996 0.004 0.000
#> TCGA-06-0210-01A-01 2 0.2255 0.8837 0.000 0.920 0.012 0.068
#> TCGA-06-0397-01A-01 2 0.0188 0.9171 0.000 0.996 0.004 0.000
#> TCGA-06-0409-01A-02 2 0.0779 0.9148 0.000 0.980 0.016 0.004
#> TCGA-06-0412-01A-01 2 0.5464 0.6762 0.000 0.716 0.212 0.072
#> TCGA-06-0644-01A-02 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.2053 0.8816 0.000 0.924 0.004 0.072
#> TCGA-08-0346-01A-01 2 0.1174 0.9116 0.000 0.968 0.020 0.012
#> TCGA-08-0352-01A-01 3 0.6503 0.0612 0.000 0.448 0.480 0.072
#> TCGA-08-0360-01A-01 2 0.0188 0.9177 0.000 0.996 0.004 0.000
#> TCGA-08-0390-01A-01 2 0.3367 0.8463 0.000 0.864 0.028 0.108
#> TCGA-08-0392-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.2053 0.8816 0.000 0.924 0.004 0.072
#> TCGA-08-0510-01A-01 2 0.6013 0.5238 0.000 0.640 0.288 0.072
#> TCGA-08-0512-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9175 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0188 0.9177 0.000 0.996 0.004 0.000
#> TCGA-12-0620-01A-01 2 0.5240 0.7174 0.000 0.740 0.188 0.072
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 4 0.3715 0.7037 0.260 0.000 0.000 0.736 0.004
#> TCGA-02-0010-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0011-01B-01 4 0.3906 0.6665 0.292 0.000 0.000 0.704 0.004
#> TCGA-02-0014-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0024-01B-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0026-01B-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0028-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0046-01A-01 4 0.3554 0.7447 0.216 0.000 0.004 0.776 0.004
#> TCGA-02-0047-01A-01 4 0.1059 0.8288 0.020 0.004 0.008 0.968 0.000
#> TCGA-02-0048-01A-01 4 0.3972 0.7491 0.212 0.000 0.008 0.764 0.016
#> TCGA-02-0060-01A-01 4 0.2130 0.8279 0.060 0.004 0.012 0.920 0.004
#> TCGA-02-0069-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0074-01A-01 1 0.0451 0.9619 0.988 0.000 0.000 0.008 0.004
#> TCGA-02-0080-01A-01 4 0.4968 0.7645 0.160 0.000 0.096 0.732 0.012
#> TCGA-02-0084-01A-03 4 0.3618 0.7685 0.004 0.004 0.168 0.808 0.016
#> TCGA-02-0087-01A-01 4 0.4421 0.7817 0.060 0.000 0.156 0.772 0.012
#> TCGA-02-0104-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0114-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0281-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0321-01A-01 4 0.3078 0.7909 0.000 0.004 0.132 0.848 0.016
#> TCGA-02-0325-01A-01 4 0.4895 0.7589 0.072 0.000 0.188 0.728 0.012
#> TCGA-02-0338-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0339-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0432-01A-02 4 0.4676 0.7320 0.220 0.000 0.032 0.728 0.020
#> TCGA-02-0439-01A-01 4 0.2837 0.8106 0.016 0.004 0.100 0.876 0.004
#> TCGA-02-0440-01A-01 1 0.0451 0.9619 0.988 0.000 0.000 0.008 0.004
#> TCGA-02-0446-01A-01 4 0.1983 0.8281 0.060 0.008 0.008 0.924 0.000
#> TCGA-06-0128-01A-01 4 0.3495 0.7824 0.152 0.000 0.000 0.816 0.032
#> TCGA-06-0129-01A-01 1 0.0451 0.9619 0.988 0.000 0.000 0.008 0.004
#> TCGA-06-0146-01A-01 1 0.1682 0.9256 0.940 0.000 0.004 0.044 0.012
#> TCGA-06-0156-01A-01 4 0.1143 0.8283 0.012 0.008 0.008 0.968 0.004
#> TCGA-06-0166-01A-01 4 0.2186 0.8228 0.016 0.044 0.012 0.924 0.004
#> TCGA-06-0174-01A-01 1 0.2338 0.8493 0.884 0.000 0.000 0.112 0.004
#> TCGA-06-0177-01A-01 1 0.0451 0.9619 0.988 0.000 0.000 0.008 0.004
#> TCGA-06-0238-01A-02 1 0.4701 0.6152 0.704 0.000 0.000 0.236 0.060
#> TCGA-06-0241-01A-02 1 0.0451 0.9619 0.988 0.000 0.000 0.008 0.004
#> TCGA-06-0410-01A-01 1 0.0451 0.9619 0.988 0.000 0.000 0.008 0.004
#> TCGA-06-0413-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-06-0414-01A-01 1 0.0451 0.9619 0.988 0.000 0.000 0.008 0.004
#> TCGA-06-0646-01A-01 4 0.3706 0.7895 0.000 0.064 0.076 0.840 0.020
#> TCGA-06-0648-01A-01 1 0.0451 0.9619 0.988 0.000 0.000 0.008 0.004
#> TCGA-08-0245-01A-01 1 0.0162 0.9641 0.996 0.000 0.000 0.000 0.004
#> TCGA-08-0344-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-08-0347-01A-01 4 0.3115 0.7989 0.012 0.008 0.120 0.856 0.004
#> TCGA-08-0348-01A-01 4 0.4743 0.5875 0.332 0.000 0.024 0.640 0.004
#> TCGA-08-0350-01A-01 1 0.2701 0.8881 0.896 0.000 0.048 0.044 0.012
#> TCGA-08-0353-01A-01 3 0.1278 0.8771 0.004 0.000 0.960 0.020 0.016
#> TCGA-08-0359-01A-01 4 0.2017 0.8275 0.060 0.004 0.008 0.924 0.004
#> TCGA-08-0385-01A-01 1 0.0510 0.9648 0.984 0.000 0.000 0.000 0.016
#> TCGA-08-0517-01A-01 1 0.0404 0.9611 0.988 0.000 0.000 0.012 0.000
#> TCGA-08-0524-01A-01 1 0.0609 0.9649 0.980 0.000 0.000 0.000 0.020
#> TCGA-12-0616-01A-01 1 0.0771 0.9560 0.976 0.000 0.000 0.020 0.004
#> TCGA-12-0618-01A-01 1 0.0451 0.9619 0.988 0.000 0.000 0.008 0.004
#> TCGA-02-0089-01A-01 3 0.6272 0.6235 0.000 0.152 0.608 0.216 0.024
#> TCGA-02-0113-01A-01 3 0.3800 0.8204 0.000 0.108 0.812 0.080 0.000
#> TCGA-02-0115-01A-01 4 0.4843 0.3586 0.000 0.008 0.328 0.640 0.024
#> TCGA-02-0451-01A-01 4 0.1564 0.8206 0.000 0.024 0.004 0.948 0.024
#> TCGA-06-0132-01A-02 4 0.1831 0.8173 0.004 0.000 0.000 0.920 0.076
#> TCGA-06-0133-01A-02 4 0.2011 0.8167 0.000 0.004 0.000 0.908 0.088
#> TCGA-06-0138-01A-02 4 0.1026 0.8231 0.000 0.004 0.004 0.968 0.024
#> TCGA-06-0160-01A-01 4 0.3110 0.8094 0.060 0.000 0.000 0.860 0.080
#> TCGA-06-0162-01A-01 4 0.2011 0.8164 0.000 0.004 0.000 0.908 0.088
#> TCGA-06-0167-01A-01 4 0.3110 0.8094 0.060 0.000 0.000 0.860 0.080
#> TCGA-06-0171-01A-02 4 0.1270 0.8219 0.000 0.000 0.000 0.948 0.052
#> TCGA-06-0173-01A-01 4 0.1865 0.8190 0.000 0.032 0.008 0.936 0.024
#> TCGA-06-0179-01A-02 4 0.1831 0.8173 0.004 0.000 0.000 0.920 0.076
#> TCGA-06-0182-01A-01 3 0.4777 0.3035 0.000 0.008 0.548 0.436 0.008
#> TCGA-06-0185-01A-01 3 0.4299 0.6083 0.000 0.008 0.672 0.316 0.004
#> TCGA-06-0195-01B-01 4 0.3119 0.8088 0.068 0.000 0.000 0.860 0.072
#> TCGA-06-0208-01B-01 4 0.5452 -0.0323 0.000 0.000 0.448 0.492 0.060
#> TCGA-06-0214-01A-02 4 0.2027 0.8166 0.000 0.040 0.008 0.928 0.024
#> TCGA-06-0219-01A-01 4 0.1671 0.8174 0.000 0.000 0.000 0.924 0.076
#> TCGA-06-0221-01A-01 4 0.5004 0.6366 0.256 0.000 0.000 0.672 0.072
#> TCGA-06-0237-01A-02 4 0.1768 0.8194 0.000 0.004 0.000 0.924 0.072
#> TCGA-06-0240-01A-02 4 0.3110 0.8094 0.060 0.000 0.000 0.860 0.080
#> TCGA-08-0349-01A-01 4 0.1087 0.8239 0.000 0.008 0.008 0.968 0.016
#> TCGA-08-0380-01A-01 4 0.0992 0.8229 0.000 0.008 0.000 0.968 0.024
#> TCGA-08-0386-01A-01 3 0.4883 0.1153 0.000 0.004 0.516 0.464 0.016
#> TCGA-08-0520-01A-01 4 0.4462 0.4462 0.000 0.004 0.308 0.672 0.016
#> TCGA-02-0007-01A-01 4 0.3819 0.7273 0.000 0.004 0.208 0.772 0.016
#> TCGA-02-0009-01A-01 3 0.0162 0.8862 0.000 0.000 0.996 0.000 0.004
#> TCGA-02-0016-01A-01 3 0.0290 0.8853 0.000 0.000 0.992 0.000 0.008
#> TCGA-02-0021-01A-01 3 0.0000 0.8869 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.1662 0.8803 0.000 0.004 0.936 0.056 0.004
#> TCGA-02-0027-01A-01 3 0.2873 0.7957 0.000 0.000 0.860 0.120 0.020
#> TCGA-02-0038-01A-01 3 0.4031 0.8088 0.000 0.124 0.804 0.064 0.008
#> TCGA-02-0043-01A-01 3 0.0162 0.8862 0.000 0.000 0.996 0.000 0.004
#> TCGA-02-0070-01A-01 3 0.0290 0.8870 0.000 0.008 0.992 0.000 0.000
#> TCGA-02-0102-01A-01 3 0.0162 0.8862 0.000 0.000 0.996 0.000 0.004
#> TCGA-02-0260-01A-03 3 0.0290 0.8853 0.000 0.000 0.992 0.000 0.008
#> TCGA-02-0269-01B-01 3 0.0290 0.8853 0.000 0.000 0.992 0.000 0.008
#> TCGA-02-0285-01A-01 3 0.1740 0.8780 0.000 0.012 0.932 0.056 0.000
#> TCGA-02-0289-01A-01 3 0.0290 0.8853 0.000 0.000 0.992 0.000 0.008
#> TCGA-02-0290-01A-01 3 0.3527 0.8224 0.000 0.116 0.828 0.056 0.000
#> TCGA-02-0317-01A-01 3 0.0290 0.8853 0.000 0.000 0.992 0.000 0.008
#> TCGA-02-0333-01A-02 3 0.0290 0.8853 0.000 0.000 0.992 0.000 0.008
#> TCGA-02-0422-01A-01 3 0.0955 0.8862 0.000 0.004 0.968 0.028 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.8869 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0162 0.8862 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0126-01A-01 3 0.0290 0.8861 0.000 0.000 0.992 0.000 0.008
#> TCGA-06-0137-01A-03 3 0.0162 0.8862 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0145-01A-04 3 0.1205 0.8840 0.000 0.004 0.956 0.040 0.000
#> TCGA-06-0148-01A-01 3 0.0162 0.8862 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0187-01A-01 3 0.3159 0.8425 0.000 0.088 0.856 0.056 0.000
#> TCGA-06-0211-01B-01 3 0.1041 0.8858 0.000 0.004 0.964 0.032 0.000
#> TCGA-06-0402-01A-01 3 0.0671 0.8874 0.000 0.004 0.980 0.016 0.000
#> TCGA-08-0246-01A-01 3 0.3669 0.8129 0.000 0.128 0.816 0.056 0.000
#> TCGA-08-0354-01A-01 3 0.4793 0.6545 0.000 0.260 0.684 0.056 0.000
#> TCGA-08-0355-01A-01 3 0.1845 0.8772 0.000 0.016 0.928 0.056 0.000
#> TCGA-08-0357-01A-01 3 0.1502 0.8796 0.000 0.004 0.940 0.056 0.000
#> TCGA-08-0358-01A-01 3 0.0740 0.8837 0.004 0.000 0.980 0.008 0.008
#> TCGA-08-0375-01A-01 3 0.0162 0.8862 0.000 0.000 0.996 0.000 0.004
#> TCGA-08-0511-01A-01 3 0.1628 0.8792 0.000 0.008 0.936 0.056 0.000
#> TCGA-08-0514-01A-01 3 0.2661 0.8604 0.000 0.056 0.888 0.056 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.8869 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.0451 0.8876 0.000 0.004 0.988 0.008 0.000
#> TCGA-08-0531-01A-01 3 0.1357 0.8822 0.000 0.004 0.948 0.048 0.000
#> TCGA-02-0057-01A-01 3 0.5824 0.6991 0.000 0.132 0.664 0.180 0.024
#> TCGA-02-0004-01A-01 5 0.2424 0.9857 0.000 0.132 0.000 0.000 0.868
#> TCGA-02-0006-01B-01 2 0.2364 0.8557 0.000 0.908 0.008 0.064 0.020
#> TCGA-02-0025-01A-01 5 0.2516 0.9782 0.000 0.140 0.000 0.000 0.860
#> TCGA-02-0033-01A-01 5 0.2424 0.9857 0.000 0.132 0.000 0.000 0.868
#> TCGA-02-0034-01A-01 5 0.2813 0.9476 0.000 0.168 0.000 0.000 0.832
#> TCGA-02-0039-01A-01 2 0.2882 0.8429 0.000 0.888 0.028 0.060 0.024
#> TCGA-02-0051-01A-01 5 0.2424 0.9857 0.000 0.132 0.000 0.000 0.868
#> TCGA-02-0054-01A-01 2 0.2139 0.8625 0.000 0.920 0.012 0.056 0.012
#> TCGA-02-0055-01A-01 5 0.2424 0.9857 0.000 0.132 0.000 0.000 0.868
#> TCGA-02-0059-01A-01 5 0.2424 0.9857 0.000 0.132 0.000 0.000 0.868
#> TCGA-02-0064-01A-01 2 0.0404 0.8873 0.000 0.988 0.000 0.000 0.012
#> TCGA-02-0075-01A-01 2 0.0404 0.8873 0.000 0.988 0.000 0.000 0.012
#> TCGA-02-0079-01A-03 2 0.2243 0.8633 0.000 0.916 0.012 0.056 0.016
#> TCGA-02-0085-01A-01 4 0.3115 0.7704 0.004 0.120 0.012 0.856 0.008
#> TCGA-02-0086-01A-01 2 0.1043 0.8712 0.000 0.960 0.000 0.000 0.040
#> TCGA-02-0099-01A-01 2 0.1740 0.8669 0.000 0.932 0.012 0.056 0.000
#> TCGA-02-0106-01A-01 2 0.2773 0.7324 0.000 0.836 0.000 0.000 0.164
#> TCGA-02-0107-01A-01 2 0.0290 0.8883 0.000 0.992 0.000 0.000 0.008
#> TCGA-02-0111-01A-01 2 0.0162 0.8893 0.000 0.996 0.000 0.000 0.004
#> TCGA-02-0326-01A-01 4 0.4988 0.3782 0.000 0.004 0.416 0.556 0.024
#> TCGA-02-0337-01A-01 4 0.4633 0.4250 0.004 0.348 0.016 0.632 0.000
#> TCGA-06-0122-01A-01 2 0.4400 0.6336 0.000 0.736 0.212 0.052 0.000
#> TCGA-06-0124-01A-01 2 0.0162 0.8893 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0130-01A-01 5 0.2424 0.9857 0.000 0.132 0.000 0.000 0.868
#> TCGA-06-0139-01A-01 5 0.2424 0.9857 0.000 0.132 0.000 0.000 0.868
#> TCGA-06-0143-01A-01 2 0.2983 0.8237 0.000 0.868 0.076 0.056 0.000
#> TCGA-06-0147-01A-01 5 0.3395 0.8591 0.000 0.236 0.000 0.000 0.764
#> TCGA-06-0149-01A-05 3 0.4708 0.7258 0.000 0.208 0.728 0.056 0.008
#> TCGA-06-0152-01A-02 3 0.2983 0.8540 0.000 0.076 0.868 0.056 0.000
#> TCGA-06-0154-01A-02 2 0.0290 0.8887 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0164-01A-01 2 0.1608 0.8432 0.000 0.928 0.000 0.000 0.072
#> TCGA-06-0175-01A-01 2 0.2866 0.8377 0.000 0.884 0.020 0.076 0.020
#> TCGA-06-0176-01A-03 5 0.2424 0.9857 0.000 0.132 0.000 0.000 0.868
#> TCGA-06-0184-01A-01 2 0.5755 0.3838 0.000 0.604 0.312 0.060 0.024
#> TCGA-06-0189-01A-05 2 0.1671 0.8401 0.000 0.924 0.000 0.000 0.076
#> TCGA-06-0190-01A-01 2 0.1478 0.8521 0.000 0.936 0.000 0.000 0.064
#> TCGA-06-0194-01A-01 2 0.0609 0.8832 0.000 0.980 0.000 0.000 0.020
#> TCGA-06-0197-01A-02 2 0.2280 0.7852 0.000 0.880 0.000 0.000 0.120
#> TCGA-06-0210-01A-01 2 0.1043 0.8797 0.000 0.960 0.000 0.040 0.000
#> TCGA-06-0397-01A-01 2 0.1043 0.8738 0.000 0.960 0.000 0.000 0.040
#> TCGA-06-0409-01A-02 2 0.0162 0.8893 0.000 0.996 0.000 0.000 0.004
#> TCGA-06-0412-01A-01 2 0.4428 0.5487 0.000 0.700 0.268 0.032 0.000
#> TCGA-06-0644-01A-02 5 0.2424 0.9857 0.000 0.132 0.000 0.000 0.868
#> TCGA-06-0645-01A-01 2 0.0609 0.8868 0.000 0.980 0.000 0.020 0.000
#> TCGA-08-0346-01A-01 2 0.0794 0.8846 0.000 0.972 0.000 0.028 0.000
#> TCGA-08-0352-01A-01 3 0.5110 0.6394 0.000 0.268 0.668 0.056 0.008
#> TCGA-08-0360-01A-01 2 0.0290 0.8887 0.000 0.992 0.000 0.000 0.008
#> TCGA-08-0390-01A-01 2 0.2321 0.8605 0.000 0.912 0.008 0.056 0.024
#> TCGA-08-0392-01A-01 5 0.2424 0.9857 0.000 0.132 0.000 0.000 0.868
#> TCGA-08-0509-01A-01 2 0.0162 0.8893 0.000 0.996 0.000 0.000 0.004
#> TCGA-08-0510-01A-01 3 0.4735 0.6363 0.000 0.284 0.672 0.044 0.000
#> TCGA-08-0512-01A-01 2 0.1270 0.8625 0.000 0.948 0.000 0.000 0.052
#> TCGA-08-0522-01A-01 5 0.2424 0.9857 0.000 0.132 0.000 0.000 0.868
#> TCGA-12-0619-01A-01 2 0.0486 0.8897 0.000 0.988 0.004 0.004 0.004
#> TCGA-12-0620-01A-01 2 0.1943 0.8639 0.000 0.924 0.020 0.056 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.5858 -0.1128 0.476 0.000 0.000 0.224 0.000 0.300
#> TCGA-02-0010-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0011-01B-01 1 0.5797 0.1140 0.528 0.000 0.004 0.244 0.000 0.224
#> TCGA-02-0014-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0024-01B-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0026-01B-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0028-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0046-01A-01 6 0.5252 0.2974 0.172 0.000 0.004 0.200 0.000 0.624
#> TCGA-02-0047-01A-01 6 0.3348 0.5778 0.000 0.016 0.000 0.216 0.000 0.768
#> TCGA-02-0048-01A-01 6 0.5085 0.4112 0.164 0.000 0.044 0.096 0.000 0.696
#> TCGA-02-0060-01A-01 6 0.3357 0.5500 0.004 0.000 0.008 0.224 0.000 0.764
#> TCGA-02-0069-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0074-01A-01 1 0.2119 0.8400 0.904 0.000 0.000 0.060 0.000 0.036
#> TCGA-02-0080-01A-01 4 0.6340 0.6203 0.128 0.000 0.096 0.568 0.000 0.208
#> TCGA-02-0084-01A-03 6 0.4795 0.5882 0.000 0.024 0.132 0.128 0.000 0.716
#> TCGA-02-0087-01A-01 6 0.4682 0.5154 0.004 0.000 0.092 0.224 0.000 0.680
#> TCGA-02-0104-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0114-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0281-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0321-01A-01 6 0.1198 0.6719 0.004 0.004 0.012 0.020 0.000 0.960
#> TCGA-02-0325-01A-01 6 0.5721 0.3614 0.008 0.000 0.208 0.224 0.000 0.560
#> TCGA-02-0338-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0339-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-02-0432-01A-02 4 0.5561 0.6494 0.124 0.000 0.032 0.624 0.000 0.220
#> TCGA-02-0439-01A-01 6 0.3470 0.6190 0.000 0.012 0.020 0.176 0.000 0.792
#> TCGA-02-0440-01A-01 1 0.2795 0.8043 0.856 0.000 0.000 0.100 0.000 0.044
#> TCGA-02-0446-01A-01 6 0.3426 0.5714 0.000 0.012 0.004 0.220 0.000 0.764
#> TCGA-06-0128-01A-01 1 0.5942 -0.2140 0.424 0.000 0.000 0.220 0.000 0.356
#> TCGA-06-0129-01A-01 1 0.1528 0.8468 0.936 0.000 0.000 0.048 0.000 0.016
#> TCGA-06-0146-01A-01 1 0.2402 0.8373 0.896 0.000 0.012 0.060 0.000 0.032
#> TCGA-06-0156-01A-01 6 0.3043 0.5869 0.004 0.000 0.004 0.196 0.000 0.796
#> TCGA-06-0166-01A-01 6 0.3074 0.5825 0.004 0.000 0.004 0.200 0.000 0.792
#> TCGA-06-0174-01A-01 1 0.3694 0.7110 0.784 0.000 0.000 0.140 0.000 0.076
#> TCGA-06-0177-01A-01 1 0.1970 0.8423 0.912 0.000 0.000 0.060 0.000 0.028
#> TCGA-06-0238-01A-02 1 0.4636 0.5942 0.692 0.000 0.000 0.160 0.000 0.148
#> TCGA-06-0241-01A-02 1 0.1921 0.8437 0.916 0.000 0.000 0.052 0.000 0.032
#> TCGA-06-0410-01A-01 1 0.2119 0.8391 0.904 0.000 0.000 0.060 0.000 0.036
#> TCGA-06-0413-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-06-0414-01A-01 1 0.2119 0.8391 0.904 0.000 0.000 0.060 0.000 0.036
#> TCGA-06-0646-01A-01 6 0.1933 0.6741 0.000 0.032 0.004 0.044 0.000 0.920
#> TCGA-06-0648-01A-01 1 0.1984 0.8424 0.912 0.000 0.000 0.056 0.000 0.032
#> TCGA-08-0245-01A-01 1 0.1398 0.8470 0.940 0.000 0.000 0.052 0.000 0.008
#> TCGA-08-0344-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-08-0347-01A-01 6 0.3296 0.6049 0.000 0.012 0.008 0.188 0.000 0.792
#> TCGA-08-0348-01A-01 6 0.5633 0.0841 0.200 0.000 0.008 0.216 0.000 0.576
#> TCGA-08-0350-01A-01 1 0.4801 0.6607 0.724 0.000 0.036 0.136 0.000 0.104
#> TCGA-08-0353-01A-01 3 0.3463 0.6411 0.004 0.000 0.748 0.000 0.008 0.240
#> TCGA-08-0359-01A-01 6 0.3248 0.5493 0.004 0.000 0.004 0.224 0.000 0.768
#> TCGA-08-0385-01A-01 1 0.0993 0.8478 0.964 0.000 0.000 0.012 0.000 0.024
#> TCGA-08-0517-01A-01 1 0.2685 0.8154 0.868 0.000 0.000 0.072 0.000 0.060
#> TCGA-08-0524-01A-01 1 0.0146 0.8468 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-12-0616-01A-01 1 0.3481 0.7384 0.792 0.000 0.000 0.160 0.000 0.048
#> TCGA-12-0618-01A-01 1 0.1890 0.8440 0.916 0.000 0.000 0.060 0.000 0.024
#> TCGA-02-0089-01A-01 3 0.5862 0.4242 0.000 0.176 0.520 0.004 0.004 0.296
#> TCGA-02-0113-01A-01 3 0.4218 0.6932 0.000 0.084 0.740 0.004 0.000 0.172
#> TCGA-02-0115-01A-01 6 0.5774 0.2023 0.000 0.064 0.356 0.052 0.000 0.528
#> TCGA-02-0451-01A-01 6 0.2633 0.6178 0.000 0.112 0.020 0.004 0.000 0.864
#> TCGA-06-0132-01A-02 6 0.3499 0.5054 0.000 0.000 0.000 0.320 0.000 0.680
#> TCGA-06-0133-01A-02 6 0.3543 0.5668 0.000 0.000 0.032 0.200 0.000 0.768
#> TCGA-06-0138-01A-02 6 0.0993 0.6689 0.000 0.012 0.000 0.024 0.000 0.964
#> TCGA-06-0160-01A-01 4 0.2146 0.7163 0.000 0.000 0.000 0.880 0.004 0.116
#> TCGA-06-0162-01A-01 6 0.3198 0.5287 0.000 0.000 0.000 0.260 0.000 0.740
#> TCGA-06-0167-01A-01 4 0.2146 0.7163 0.000 0.000 0.000 0.880 0.004 0.116
#> TCGA-06-0171-01A-02 6 0.1814 0.6632 0.000 0.000 0.000 0.100 0.000 0.900
#> TCGA-06-0173-01A-01 6 0.0777 0.6715 0.000 0.024 0.004 0.000 0.000 0.972
#> TCGA-06-0179-01A-02 6 0.3482 0.5080 0.000 0.000 0.000 0.316 0.000 0.684
#> TCGA-06-0182-01A-01 6 0.4393 -0.0314 0.000 0.016 0.480 0.004 0.000 0.500
#> TCGA-06-0185-01A-01 3 0.4523 0.3754 0.000 0.032 0.592 0.004 0.000 0.372
#> TCGA-06-0195-01B-01 4 0.6117 0.3366 0.344 0.000 0.000 0.356 0.000 0.300
#> TCGA-06-0208-01B-01 6 0.4487 0.3994 0.000 0.000 0.264 0.068 0.000 0.668
#> TCGA-06-0214-01A-02 6 0.1411 0.6623 0.000 0.060 0.004 0.000 0.000 0.936
#> TCGA-06-0219-01A-01 6 0.3426 0.5414 0.004 0.000 0.000 0.276 0.000 0.720
#> TCGA-06-0221-01A-01 1 0.5147 -0.0373 0.480 0.000 0.000 0.436 0.000 0.084
#> TCGA-06-0237-01A-02 6 0.1616 0.6627 0.000 0.000 0.020 0.048 0.000 0.932
#> TCGA-06-0240-01A-02 4 0.2146 0.7163 0.000 0.000 0.000 0.880 0.004 0.116
#> TCGA-08-0349-01A-01 6 0.0363 0.6704 0.000 0.012 0.000 0.000 0.000 0.988
#> TCGA-08-0380-01A-01 6 0.2957 0.6407 0.000 0.064 0.016 0.056 0.000 0.864
#> TCGA-08-0386-01A-01 6 0.2520 0.5690 0.000 0.000 0.152 0.004 0.000 0.844
#> TCGA-08-0520-01A-01 6 0.3427 0.5467 0.000 0.032 0.156 0.008 0.000 0.804
#> TCGA-02-0007-01A-01 6 0.1555 0.6578 0.004 0.000 0.060 0.000 0.004 0.932
#> TCGA-02-0009-01A-01 3 0.2070 0.8172 0.000 0.000 0.892 0.100 0.008 0.000
#> TCGA-02-0016-01A-01 3 0.2118 0.8163 0.000 0.000 0.888 0.104 0.008 0.000
#> TCGA-02-0021-01A-01 3 0.1769 0.8324 0.000 0.012 0.924 0.060 0.004 0.000
#> TCGA-02-0023-01B-01 3 0.2209 0.8109 0.000 0.040 0.904 0.004 0.000 0.052
#> TCGA-02-0027-01A-01 3 0.3109 0.6574 0.000 0.000 0.772 0.004 0.000 0.224
#> TCGA-02-0038-01A-01 3 0.3821 0.7362 0.000 0.156 0.776 0.004 0.000 0.064
#> TCGA-02-0043-01A-01 3 0.0547 0.8328 0.000 0.020 0.980 0.000 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.1501 0.8162 0.000 0.076 0.924 0.000 0.000 0.000
#> TCGA-02-0102-01A-01 3 0.0725 0.8333 0.000 0.012 0.976 0.012 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.1757 0.8267 0.000 0.000 0.916 0.076 0.008 0.000
#> TCGA-02-0269-01B-01 3 0.2118 0.8163 0.000 0.000 0.888 0.104 0.008 0.000
#> TCGA-02-0285-01A-01 3 0.2144 0.8077 0.000 0.092 0.896 0.004 0.004 0.004
#> TCGA-02-0289-01A-01 3 0.2118 0.8163 0.000 0.000 0.888 0.104 0.008 0.000
#> TCGA-02-0290-01A-01 3 0.3820 0.5448 0.000 0.332 0.660 0.000 0.004 0.004
#> TCGA-02-0317-01A-01 3 0.2118 0.8163 0.000 0.000 0.888 0.104 0.008 0.000
#> TCGA-02-0333-01A-02 3 0.2118 0.8163 0.000 0.000 0.888 0.104 0.008 0.000
#> TCGA-02-0422-01A-01 3 0.0458 0.8319 0.000 0.016 0.984 0.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.0508 0.8323 0.000 0.012 0.984 0.004 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.1970 0.8209 0.000 0.000 0.900 0.092 0.008 0.000
#> TCGA-06-0126-01A-01 3 0.1845 0.8276 0.000 0.000 0.916 0.072 0.008 0.004
#> TCGA-06-0137-01A-03 3 0.2070 0.8172 0.000 0.000 0.892 0.100 0.008 0.000
#> TCGA-06-0145-01A-04 3 0.2653 0.8248 0.000 0.028 0.868 0.100 0.004 0.000
#> TCGA-06-0148-01A-01 3 0.0547 0.8329 0.000 0.020 0.980 0.000 0.000 0.000
#> TCGA-06-0187-01A-01 3 0.2848 0.7530 0.000 0.176 0.816 0.000 0.000 0.008
#> TCGA-06-0211-01B-01 3 0.2513 0.7726 0.000 0.000 0.852 0.000 0.008 0.140
#> TCGA-06-0402-01A-01 3 0.0632 0.8327 0.000 0.024 0.976 0.000 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.3451 0.7232 0.000 0.204 0.776 0.004 0.004 0.012
#> TCGA-08-0354-01A-01 3 0.4252 0.3937 0.000 0.396 0.588 0.004 0.004 0.008
#> TCGA-08-0355-01A-01 3 0.3231 0.7785 0.000 0.092 0.840 0.004 0.004 0.060
#> TCGA-08-0357-01A-01 3 0.0665 0.8329 0.000 0.008 0.980 0.000 0.008 0.004
#> TCGA-08-0358-01A-01 3 0.2429 0.7896 0.008 0.000 0.888 0.008 0.008 0.088
#> TCGA-08-0375-01A-01 3 0.1333 0.8315 0.000 0.000 0.944 0.048 0.008 0.000
#> TCGA-08-0511-01A-01 3 0.2132 0.8321 0.000 0.052 0.912 0.028 0.004 0.004
#> TCGA-08-0514-01A-01 3 0.2773 0.7694 0.000 0.152 0.836 0.000 0.004 0.008
#> TCGA-08-0518-01A-01 3 0.2170 0.8225 0.000 0.012 0.888 0.100 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.2006 0.8300 0.000 0.016 0.904 0.080 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.2325 0.8201 0.000 0.008 0.884 0.100 0.008 0.000
#> TCGA-02-0057-01A-01 3 0.5816 0.3344 0.000 0.148 0.496 0.004 0.004 0.348
#> TCGA-02-0004-01A-01 5 0.1267 0.9473 0.000 0.060 0.000 0.000 0.940 0.000
#> TCGA-02-0006-01B-01 2 0.0260 0.8766 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-02-0025-01A-01 5 0.0865 0.9755 0.000 0.036 0.000 0.000 0.964 0.000
#> TCGA-02-0033-01A-01 5 0.0632 0.9887 0.000 0.024 0.000 0.000 0.976 0.000
#> TCGA-02-0034-01A-01 5 0.1444 0.9270 0.000 0.072 0.000 0.000 0.928 0.000
#> TCGA-02-0039-01A-01 2 0.1036 0.8664 0.000 0.964 0.024 0.000 0.004 0.008
#> TCGA-02-0051-01A-01 5 0.0632 0.9887 0.000 0.024 0.000 0.000 0.976 0.000
#> TCGA-02-0054-01A-01 2 0.0291 0.8771 0.000 0.992 0.004 0.000 0.000 0.004
#> TCGA-02-0055-01A-01 5 0.0632 0.9887 0.000 0.024 0.000 0.000 0.976 0.000
#> TCGA-02-0059-01A-01 5 0.0632 0.9887 0.000 0.024 0.000 0.000 0.976 0.000
#> TCGA-02-0064-01A-01 2 0.1152 0.8726 0.000 0.952 0.000 0.004 0.044 0.000
#> TCGA-02-0075-01A-01 2 0.1219 0.8706 0.000 0.948 0.000 0.004 0.048 0.000
#> TCGA-02-0079-01A-03 2 0.0551 0.8769 0.000 0.984 0.004 0.000 0.008 0.004
#> TCGA-02-0085-01A-01 6 0.4150 0.5885 0.000 0.148 0.004 0.084 0.004 0.760
#> TCGA-02-0086-01A-01 2 0.1908 0.8418 0.000 0.900 0.000 0.004 0.096 0.000
#> TCGA-02-0099-01A-01 2 0.0146 0.8774 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0106-01A-01 2 0.3872 0.3701 0.000 0.604 0.000 0.004 0.392 0.000
#> TCGA-02-0107-01A-01 2 0.1007 0.8732 0.000 0.956 0.000 0.000 0.044 0.000
#> TCGA-02-0111-01A-01 2 0.0632 0.8787 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-02-0326-01A-01 6 0.3534 0.4403 0.000 0.000 0.276 0.008 0.000 0.716
#> TCGA-02-0337-01A-01 2 0.5692 0.0558 0.000 0.512 0.000 0.136 0.008 0.344
#> TCGA-06-0122-01A-01 2 0.2053 0.8122 0.000 0.888 0.108 0.000 0.000 0.004
#> TCGA-06-0124-01A-01 2 0.0777 0.8786 0.000 0.972 0.000 0.004 0.024 0.000
#> TCGA-06-0130-01A-01 5 0.0632 0.9887 0.000 0.024 0.000 0.000 0.976 0.000
#> TCGA-06-0139-01A-01 5 0.0632 0.9887 0.000 0.024 0.000 0.000 0.976 0.000
#> TCGA-06-0143-01A-01 2 0.0653 0.8743 0.000 0.980 0.012 0.000 0.004 0.004
#> TCGA-06-0147-01A-01 5 0.0632 0.9887 0.000 0.024 0.000 0.000 0.976 0.000
#> TCGA-06-0149-01A-05 2 0.4014 0.4022 0.000 0.640 0.348 0.004 0.004 0.004
#> TCGA-06-0152-01A-02 3 0.4280 0.6667 0.000 0.232 0.708 0.004 0.000 0.056
#> TCGA-06-0154-01A-02 2 0.1010 0.8755 0.000 0.960 0.000 0.004 0.036 0.000
#> TCGA-06-0164-01A-01 2 0.2520 0.7870 0.000 0.844 0.000 0.004 0.152 0.000
#> TCGA-06-0175-01A-01 2 0.2376 0.8203 0.000 0.888 0.068 0.000 0.000 0.044
#> TCGA-06-0176-01A-03 5 0.0632 0.9887 0.000 0.024 0.000 0.000 0.976 0.000
#> TCGA-06-0184-01A-01 2 0.3691 0.7118 0.000 0.780 0.168 0.004 0.000 0.048
#> TCGA-06-0189-01A-05 2 0.2234 0.8157 0.000 0.872 0.000 0.004 0.124 0.000
#> TCGA-06-0190-01A-01 2 0.2442 0.7958 0.000 0.852 0.000 0.004 0.144 0.000
#> TCGA-06-0194-01A-01 2 0.1411 0.8640 0.000 0.936 0.000 0.004 0.060 0.000
#> TCGA-06-0197-01A-02 2 0.3290 0.6590 0.000 0.744 0.000 0.004 0.252 0.000
#> TCGA-06-0210-01A-01 2 0.0146 0.8774 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-06-0397-01A-01 2 0.1806 0.8468 0.000 0.908 0.000 0.004 0.088 0.000
#> TCGA-06-0409-01A-02 2 0.0713 0.8782 0.000 0.972 0.000 0.000 0.028 0.000
#> TCGA-06-0412-01A-01 2 0.3074 0.7209 0.000 0.792 0.200 0.000 0.004 0.004
#> TCGA-06-0644-01A-02 5 0.0632 0.9887 0.000 0.024 0.000 0.000 0.976 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.8784 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0291 0.8793 0.000 0.992 0.000 0.004 0.004 0.000
#> TCGA-08-0352-01A-01 2 0.3054 0.7337 0.000 0.808 0.180 0.004 0.004 0.004
#> TCGA-08-0360-01A-01 2 0.0858 0.8779 0.000 0.968 0.000 0.004 0.028 0.000
#> TCGA-08-0390-01A-01 2 0.1285 0.8538 0.000 0.944 0.000 0.000 0.004 0.052
#> TCGA-08-0392-01A-01 5 0.0632 0.9887 0.000 0.024 0.000 0.000 0.976 0.000
#> TCGA-08-0509-01A-01 2 0.0146 0.8790 0.000 0.996 0.000 0.000 0.004 0.000
#> TCGA-08-0510-01A-01 2 0.3332 0.6935 0.000 0.772 0.216 0.004 0.004 0.004
#> TCGA-08-0512-01A-01 2 0.2053 0.8287 0.000 0.888 0.000 0.004 0.108 0.000
#> TCGA-08-0522-01A-01 5 0.0632 0.9887 0.000 0.024 0.000 0.000 0.976 0.000
#> TCGA-12-0619-01A-01 2 0.0603 0.8796 0.000 0.980 0.000 0.004 0.016 0.000
#> TCGA-12-0620-01A-01 2 0.0551 0.8739 0.000 0.984 0.008 0.000 0.004 0.004
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> MAD:mclust 165 5.26e-33 2
#> MAD:mclust 142 9.15e-56 3
#> MAD:mclust 154 2.09e-64 4
#> MAD:mclust 165 2.45e-58 5
#> MAD:mclust 153 1.71e-61 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "NMF"]
# you can also extract it by
# res = res_list["MAD:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.893 0.927 0.969 0.4933 0.503 0.503
#> 3 3 0.616 0.652 0.769 0.3313 0.765 0.565
#> 4 4 0.921 0.913 0.962 0.1408 0.832 0.560
#> 5 5 0.789 0.732 0.841 0.0419 0.937 0.763
#> 6 6 0.738 0.660 0.807 0.0358 0.964 0.843
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.3733 0.898 0.928 0.072
#> TCGA-02-0048-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0084-01A-03 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0087-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0104-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.8327 0.675 0.736 0.264
#> TCGA-02-0325-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.7219 0.759 0.800 0.200
#> TCGA-06-0128-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.8955 0.587 0.688 0.312
#> TCGA-06-0166-01A-01 1 0.3114 0.912 0.944 0.056
#> TCGA-06-0174-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0238-01A-02 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.0376 0.976 0.004 0.996
#> TCGA-06-0648-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.0938 0.945 0.988 0.012
#> TCGA-08-0348-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0353-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0115-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0138-01A-02 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0171-01A-02 1 0.9087 0.554 0.676 0.324
#> TCGA-06-0173-01A-01 2 0.3274 0.918 0.060 0.940
#> TCGA-06-0179-01A-02 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0185-01A-01 2 0.0672 0.972 0.008 0.992
#> TCGA-06-0195-01B-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.3274 0.919 0.060 0.940
#> TCGA-06-0214-01A-02 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.7453 0.715 0.212 0.788
#> TCGA-06-0221-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0237-01A-02 1 0.1633 0.937 0.976 0.024
#> TCGA-06-0240-01A-02 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0349-01A-01 1 0.9850 0.304 0.572 0.428
#> TCGA-08-0380-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0520-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0007-01A-01 1 0.1414 0.939 0.980 0.020
#> TCGA-02-0009-01A-01 1 0.7528 0.743 0.784 0.216
#> TCGA-02-0016-01A-01 1 0.1184 0.942 0.984 0.016
#> TCGA-02-0021-01A-01 2 0.9608 0.331 0.384 0.616
#> TCGA-02-0023-01B-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.8016 0.704 0.756 0.244
#> TCGA-02-0038-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0043-01A-01 1 0.9732 0.373 0.596 0.404
#> TCGA-02-0070-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0102-01A-01 2 0.9896 0.156 0.440 0.560
#> TCGA-02-0260-01A-03 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0269-01B-01 1 0.0000 0.952 1.000 0.000
#> TCGA-02-0285-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0289-01A-01 1 0.5737 0.839 0.864 0.136
#> TCGA-02-0290-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0317-01A-01 1 0.6438 0.809 0.836 0.164
#> TCGA-02-0333-01A-02 1 0.6048 0.826 0.852 0.148
#> TCGA-02-0422-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0430-01A-01 2 0.9922 0.126 0.448 0.552
#> TCGA-06-0125-01A-01 1 0.6048 0.826 0.852 0.148
#> TCGA-06-0126-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0137-01A-03 1 0.0000 0.952 1.000 0.000
#> TCGA-06-0145-01A-04 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0148-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0187-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0211-01B-01 1 0.0376 0.950 0.996 0.004
#> TCGA-06-0402-01A-01 2 0.6712 0.766 0.176 0.824
#> TCGA-08-0246-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0357-01A-01 1 0.9358 0.507 0.648 0.352
#> TCGA-08-0358-01A-01 1 0.0000 0.952 1.000 0.000
#> TCGA-08-0375-01A-01 1 0.0376 0.950 0.996 0.004
#> TCGA-08-0511-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0514-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0529-01A-02 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0531-01A-01 2 0.0938 0.968 0.012 0.988
#> TCGA-02-0057-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-02-0337-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0147-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.980 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.980 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.980 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.6062 0.7333 0.616 0.000 0.384
#> TCGA-02-0010-01A-01 1 0.6192 0.7104 0.580 0.000 0.420
#> TCGA-02-0011-01B-01 1 0.5016 0.7448 0.760 0.000 0.240
#> TCGA-02-0014-01A-01 1 0.6126 0.7244 0.600 0.000 0.400
#> TCGA-02-0024-01B-01 1 0.6095 0.7288 0.608 0.000 0.392
#> TCGA-02-0026-01B-01 1 0.6079 0.7305 0.612 0.000 0.388
#> TCGA-02-0028-01A-01 3 0.6305 -0.5820 0.484 0.000 0.516
#> TCGA-02-0046-01A-01 1 0.6274 0.6670 0.544 0.000 0.456
#> TCGA-02-0047-01A-01 1 0.0000 0.6881 1.000 0.000 0.000
#> TCGA-02-0048-01A-01 3 0.5291 0.0863 0.268 0.000 0.732
#> TCGA-02-0060-01A-01 1 0.0237 0.6900 0.996 0.000 0.004
#> TCGA-02-0069-01A-01 1 0.6215 0.7026 0.572 0.000 0.428
#> TCGA-02-0074-01A-01 1 0.5988 0.7375 0.632 0.000 0.368
#> TCGA-02-0080-01A-01 1 0.4605 0.7379 0.796 0.000 0.204
#> TCGA-02-0084-01A-03 2 0.6045 0.5562 0.380 0.620 0.000
#> TCGA-02-0087-01A-01 1 0.0237 0.6900 0.996 0.000 0.004
#> TCGA-02-0104-01A-01 1 0.5882 0.7434 0.652 0.000 0.348
#> TCGA-02-0114-01A-01 1 0.6204 0.7070 0.576 0.000 0.424
#> TCGA-02-0281-01A-01 1 0.6291 0.6500 0.532 0.000 0.468
#> TCGA-02-0321-01A-01 1 0.8419 0.6279 0.504 0.088 0.408
#> TCGA-02-0325-01A-01 3 0.6305 -0.5605 0.484 0.000 0.516
#> TCGA-02-0338-01A-01 1 0.6204 0.7070 0.576 0.000 0.424
#> TCGA-02-0339-01A-01 1 0.6168 0.7166 0.588 0.000 0.412
#> TCGA-02-0432-01A-02 1 0.0237 0.6900 0.996 0.000 0.004
#> TCGA-02-0439-01A-01 1 0.0237 0.6900 0.996 0.000 0.004
#> TCGA-02-0440-01A-01 1 0.6062 0.7325 0.616 0.000 0.384
#> TCGA-02-0446-01A-01 1 0.0000 0.6881 1.000 0.000 0.000
#> TCGA-06-0128-01A-01 1 0.0237 0.6900 0.996 0.000 0.004
#> TCGA-06-0129-01A-01 1 0.5327 0.7474 0.728 0.000 0.272
#> TCGA-06-0146-01A-01 1 0.5216 0.7464 0.740 0.000 0.260
#> TCGA-06-0156-01A-01 1 0.7211 0.6037 0.716 0.156 0.128
#> TCGA-06-0166-01A-01 1 0.6301 0.7402 0.712 0.028 0.260
#> TCGA-06-0174-01A-01 1 0.6204 0.7070 0.576 0.000 0.424
#> TCGA-06-0177-01A-01 1 0.5706 0.7469 0.680 0.000 0.320
#> TCGA-06-0238-01A-02 1 0.0000 0.6881 1.000 0.000 0.000
#> TCGA-06-0241-01A-02 1 0.6062 0.7333 0.616 0.000 0.384
#> TCGA-06-0410-01A-01 1 0.6111 0.7252 0.604 0.000 0.396
#> TCGA-06-0413-01A-01 1 0.6180 0.7139 0.584 0.000 0.416
#> TCGA-06-0414-01A-01 1 0.5497 0.7491 0.708 0.000 0.292
#> TCGA-06-0646-01A-01 2 0.0424 0.8411 0.000 0.992 0.008
#> TCGA-06-0648-01A-01 1 0.5760 0.7464 0.672 0.000 0.328
#> TCGA-08-0245-01A-01 1 0.6204 0.7070 0.576 0.000 0.424
#> TCGA-08-0344-01A-01 1 0.6095 0.7288 0.608 0.000 0.392
#> TCGA-08-0347-01A-01 1 0.0747 0.6933 0.984 0.000 0.016
#> TCGA-08-0348-01A-01 1 0.4235 0.7328 0.824 0.000 0.176
#> TCGA-08-0350-01A-01 1 0.5733 0.7463 0.676 0.000 0.324
#> TCGA-08-0353-01A-01 3 0.0000 0.6958 0.000 0.000 1.000
#> TCGA-08-0359-01A-01 1 0.0237 0.6900 0.996 0.000 0.004
#> TCGA-08-0385-01A-01 1 0.6126 0.7244 0.600 0.000 0.400
#> TCGA-08-0517-01A-01 1 0.6204 0.7070 0.576 0.000 0.424
#> TCGA-08-0524-01A-01 1 0.6204 0.7070 0.576 0.000 0.424
#> TCGA-12-0616-01A-01 1 0.6204 0.7070 0.576 0.000 0.424
#> TCGA-12-0618-01A-01 1 0.5988 0.7376 0.632 0.000 0.368
#> TCGA-02-0089-01A-01 2 0.3816 0.7508 0.148 0.852 0.000
#> TCGA-02-0113-01A-01 2 0.6520 -0.1760 0.004 0.508 0.488
#> TCGA-02-0115-01A-01 2 0.6140 0.5262 0.404 0.596 0.000
#> TCGA-02-0451-01A-01 2 0.5859 0.5914 0.344 0.656 0.000
#> TCGA-06-0132-01A-02 2 0.6204 0.4968 0.424 0.576 0.000
#> TCGA-06-0133-01A-02 2 0.6302 0.3959 0.480 0.520 0.000
#> TCGA-06-0138-01A-02 2 0.6286 0.4246 0.464 0.536 0.000
#> TCGA-06-0160-01A-01 1 0.0000 0.6881 1.000 0.000 0.000
#> TCGA-06-0162-01A-01 2 0.6204 0.4968 0.424 0.576 0.000
#> TCGA-06-0167-01A-01 1 0.0000 0.6881 1.000 0.000 0.000
#> TCGA-06-0171-01A-02 1 0.0237 0.6854 0.996 0.004 0.000
#> TCGA-06-0173-01A-01 2 0.5397 0.6492 0.280 0.720 0.000
#> TCGA-06-0179-01A-02 2 0.6215 0.4899 0.428 0.572 0.000
#> TCGA-06-0182-01A-01 2 0.8209 -0.1480 0.072 0.472 0.456
#> TCGA-06-0185-01A-01 3 0.9142 0.3672 0.324 0.164 0.512
#> TCGA-06-0195-01B-01 1 0.0000 0.6881 1.000 0.000 0.000
#> TCGA-06-0208-01B-01 1 0.9713 -0.2298 0.404 0.220 0.376
#> TCGA-06-0214-01A-02 2 0.5835 0.5949 0.340 0.660 0.000
#> TCGA-06-0219-01A-01 1 0.1753 0.6473 0.952 0.048 0.000
#> TCGA-06-0221-01A-01 1 0.0000 0.6881 1.000 0.000 0.000
#> TCGA-06-0237-01A-02 1 0.0424 0.6826 0.992 0.008 0.000
#> TCGA-06-0240-01A-02 1 0.0000 0.6881 1.000 0.000 0.000
#> TCGA-08-0349-01A-01 1 0.2261 0.6319 0.932 0.068 0.000
#> TCGA-08-0380-01A-01 2 0.6062 0.5536 0.384 0.616 0.000
#> TCGA-08-0386-01A-01 3 0.1964 0.6232 0.056 0.000 0.944
#> TCGA-08-0520-01A-01 2 0.6427 0.5803 0.348 0.640 0.012
#> TCGA-02-0007-01A-01 3 0.0747 0.6780 0.016 0.000 0.984
#> TCGA-02-0009-01A-01 3 0.0237 0.6987 0.000 0.004 0.996
#> TCGA-02-0016-01A-01 3 0.0237 0.6949 0.004 0.000 0.996
#> TCGA-02-0021-01A-01 3 0.0424 0.6993 0.000 0.008 0.992
#> TCGA-02-0023-01B-01 3 0.7276 0.3639 0.032 0.404 0.564
#> TCGA-02-0027-01A-01 3 0.0747 0.6947 0.000 0.016 0.984
#> TCGA-02-0038-01A-01 3 0.6305 0.2248 0.000 0.484 0.516
#> TCGA-02-0043-01A-01 3 0.0237 0.6987 0.000 0.004 0.996
#> TCGA-02-0070-01A-01 3 0.5968 0.4686 0.000 0.364 0.636
#> TCGA-02-0102-01A-01 3 0.0237 0.6987 0.000 0.004 0.996
#> TCGA-02-0260-01A-03 3 0.0000 0.6958 0.000 0.000 1.000
#> TCGA-02-0269-01B-01 3 0.0000 0.6958 0.000 0.000 1.000
#> TCGA-02-0285-01A-01 3 0.6204 0.3638 0.000 0.424 0.576
#> TCGA-02-0289-01A-01 3 0.0237 0.6987 0.000 0.004 0.996
#> TCGA-02-0290-01A-01 3 0.6126 0.4083 0.000 0.400 0.600
#> TCGA-02-0317-01A-01 3 0.0237 0.6987 0.000 0.004 0.996
#> TCGA-02-0333-01A-02 3 0.0237 0.6987 0.000 0.004 0.996
#> TCGA-02-0422-01A-01 3 0.3686 0.6763 0.000 0.140 0.860
#> TCGA-02-0430-01A-01 3 0.0424 0.6993 0.000 0.008 0.992
#> TCGA-06-0125-01A-01 3 0.0237 0.6987 0.000 0.004 0.996
#> TCGA-06-0126-01A-01 3 0.0000 0.6958 0.000 0.000 1.000
#> TCGA-06-0137-01A-03 3 0.0000 0.6958 0.000 0.000 1.000
#> TCGA-06-0145-01A-04 3 0.6045 0.4424 0.000 0.380 0.620
#> TCGA-06-0148-01A-01 3 0.5968 0.4690 0.000 0.364 0.636
#> TCGA-06-0187-01A-01 3 0.6204 0.3638 0.000 0.424 0.576
#> TCGA-06-0211-01B-01 3 0.0000 0.6958 0.000 0.000 1.000
#> TCGA-06-0402-01A-01 3 0.1163 0.6975 0.000 0.028 0.972
#> TCGA-08-0246-01A-01 2 0.6307 -0.1726 0.000 0.512 0.488
#> TCGA-08-0354-01A-01 3 0.6309 0.1825 0.000 0.500 0.500
#> TCGA-08-0355-01A-01 3 0.6291 0.2636 0.000 0.468 0.532
#> TCGA-08-0357-01A-01 3 0.0237 0.6987 0.000 0.004 0.996
#> TCGA-08-0358-01A-01 3 0.0000 0.6958 0.000 0.000 1.000
#> TCGA-08-0375-01A-01 3 0.0000 0.6958 0.000 0.000 1.000
#> TCGA-08-0511-01A-01 3 0.6192 0.3720 0.000 0.420 0.580
#> TCGA-08-0514-01A-01 3 0.6215 0.3554 0.000 0.428 0.572
#> TCGA-08-0518-01A-01 3 0.4346 0.6641 0.000 0.184 0.816
#> TCGA-08-0529-01A-02 3 0.5254 0.5935 0.000 0.264 0.736
#> TCGA-08-0531-01A-01 3 0.3879 0.6735 0.000 0.152 0.848
#> TCGA-02-0057-01A-01 2 0.3482 0.7642 0.128 0.872 0.000
#> TCGA-02-0004-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.0237 0.8444 0.004 0.996 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-02-0039-01A-01 2 0.0237 0.8444 0.004 0.996 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-02-0054-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-02-0075-01A-01 2 0.1964 0.8046 0.000 0.944 0.056
#> TCGA-02-0079-01A-03 2 0.0237 0.8444 0.004 0.996 0.000
#> TCGA-02-0085-01A-01 2 0.5948 0.5777 0.360 0.640 0.000
#> TCGA-02-0086-01A-01 2 0.0237 0.8435 0.000 0.996 0.004
#> TCGA-02-0099-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-02-0106-01A-01 2 0.1163 0.8272 0.000 0.972 0.028
#> TCGA-02-0107-01A-01 2 0.0237 0.8444 0.004 0.996 0.000
#> TCGA-02-0111-01A-01 2 0.0237 0.8444 0.004 0.996 0.000
#> TCGA-02-0326-01A-01 2 0.8505 0.5300 0.256 0.600 0.144
#> TCGA-02-0337-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0122-01A-01 2 0.4654 0.6214 0.000 0.792 0.208
#> TCGA-06-0124-01A-01 2 0.2537 0.7816 0.000 0.920 0.080
#> TCGA-06-0130-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0237 0.8444 0.004 0.996 0.000
#> TCGA-06-0143-01A-01 2 0.4062 0.6859 0.000 0.836 0.164
#> TCGA-06-0147-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0152-01A-02 2 0.6305 -0.1637 0.000 0.516 0.484
#> TCGA-06-0154-01A-02 2 0.4452 0.6349 0.000 0.808 0.192
#> TCGA-06-0164-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 2 0.0424 0.8410 0.000 0.992 0.008
#> TCGA-06-0176-01A-03 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.0237 0.8444 0.004 0.996 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0197-01A-02 2 0.0237 0.8444 0.004 0.996 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0397-01A-01 2 0.0592 0.8385 0.000 0.988 0.012
#> TCGA-06-0409-01A-02 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0412-01A-01 2 0.6295 -0.1169 0.000 0.528 0.472
#> TCGA-06-0644-01A-02 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-08-0352-01A-01 2 0.0237 0.8434 0.000 0.996 0.004
#> TCGA-08-0360-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.0237 0.8444 0.004 0.996 0.000
#> TCGA-08-0392-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 2 0.3551 0.7242 0.000 0.868 0.132
#> TCGA-08-0512-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.8455 0.000 1.000 0.000
#> TCGA-12-0620-01A-01 2 0.0424 0.8410 0.000 0.992 0.008
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0010-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0011-01B-01 1 0.3444 0.7677 0.816 0.000 0.000 0.184
#> TCGA-02-0014-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0024-01B-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0026-01B-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0028-01A-01 1 0.0376 0.9649 0.992 0.000 0.004 0.004
#> TCGA-02-0046-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0047-01A-01 4 0.0336 0.9604 0.008 0.000 0.000 0.992
#> TCGA-02-0048-01A-01 3 0.4907 0.2918 0.420 0.000 0.580 0.000
#> TCGA-02-0060-01A-01 4 0.0707 0.9545 0.020 0.000 0.000 0.980
#> TCGA-02-0069-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0074-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0080-01A-01 4 0.2888 0.8529 0.124 0.000 0.004 0.872
#> TCGA-02-0084-01A-03 4 0.1994 0.9238 0.004 0.008 0.052 0.936
#> TCGA-02-0087-01A-01 4 0.0469 0.9589 0.012 0.000 0.000 0.988
#> TCGA-02-0104-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0114-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0281-01A-01 1 0.0376 0.9649 0.992 0.000 0.004 0.004
#> TCGA-02-0321-01A-01 1 0.0376 0.9649 0.992 0.000 0.004 0.004
#> TCGA-02-0325-01A-01 1 0.4283 0.6411 0.740 0.000 0.256 0.004
#> TCGA-02-0338-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0339-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0432-01A-02 4 0.1302 0.9371 0.044 0.000 0.000 0.956
#> TCGA-02-0439-01A-01 4 0.0336 0.9604 0.008 0.000 0.000 0.992
#> TCGA-02-0440-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-02-0446-01A-01 1 0.4991 0.3600 0.608 0.004 0.000 0.388
#> TCGA-06-0128-01A-01 4 0.1211 0.9403 0.040 0.000 0.000 0.960
#> TCGA-06-0129-01A-01 1 0.0469 0.9575 0.988 0.000 0.000 0.012
#> TCGA-06-0146-01A-01 1 0.2868 0.8334 0.864 0.000 0.000 0.136
#> TCGA-06-0156-01A-01 1 0.2973 0.8137 0.856 0.144 0.000 0.000
#> TCGA-06-0166-01A-01 1 0.0000 0.9651 1.000 0.000 0.000 0.000
#> TCGA-06-0174-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9651 1.000 0.000 0.000 0.000
#> TCGA-06-0238-01A-02 4 0.0336 0.9604 0.008 0.000 0.000 0.992
#> TCGA-06-0241-01A-02 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-06-0410-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-06-0413-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9651 1.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 2 0.0657 0.9462 0.012 0.984 0.000 0.004
#> TCGA-06-0648-01A-01 1 0.0000 0.9651 1.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9651 1.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 4 0.2408 0.8800 0.104 0.000 0.000 0.896
#> TCGA-08-0348-01A-01 1 0.0336 0.9605 0.992 0.000 0.000 0.008
#> TCGA-08-0350-01A-01 1 0.0188 0.9630 0.996 0.000 0.000 0.004
#> TCGA-08-0353-01A-01 3 0.3791 0.7437 0.200 0.000 0.796 0.004
#> TCGA-08-0359-01A-01 4 0.0469 0.9589 0.012 0.000 0.000 0.988
#> TCGA-08-0385-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-08-0517-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-08-0524-01A-01 1 0.0188 0.9668 0.996 0.000 0.004 0.000
#> TCGA-12-0616-01A-01 1 0.0376 0.9649 0.992 0.000 0.004 0.004
#> TCGA-12-0618-01A-01 1 0.0000 0.9651 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 4 0.0336 0.9582 0.000 0.008 0.000 0.992
#> TCGA-02-0113-01A-01 3 0.2149 0.8817 0.000 0.000 0.912 0.088
#> TCGA-02-0115-01A-01 4 0.0188 0.9598 0.000 0.000 0.004 0.996
#> TCGA-02-0451-01A-01 4 0.0188 0.9602 0.000 0.004 0.000 0.996
#> TCGA-06-0132-01A-02 4 0.0376 0.9601 0.004 0.004 0.000 0.992
#> TCGA-06-0133-01A-02 4 0.0188 0.9598 0.000 0.000 0.004 0.996
#> TCGA-06-0138-01A-02 4 0.0188 0.9602 0.000 0.004 0.000 0.996
#> TCGA-06-0160-01A-01 4 0.0336 0.9604 0.008 0.000 0.000 0.992
#> TCGA-06-0162-01A-01 4 0.0188 0.9602 0.000 0.004 0.000 0.996
#> TCGA-06-0167-01A-01 4 0.0336 0.9604 0.008 0.000 0.000 0.992
#> TCGA-06-0171-01A-02 4 0.0188 0.9607 0.004 0.000 0.000 0.996
#> TCGA-06-0173-01A-01 4 0.2921 0.8269 0.000 0.140 0.000 0.860
#> TCGA-06-0179-01A-02 4 0.0188 0.9602 0.000 0.004 0.000 0.996
#> TCGA-06-0182-01A-01 3 0.6548 0.5646 0.000 0.188 0.636 0.176
#> TCGA-06-0185-01A-01 3 0.4624 0.4958 0.000 0.000 0.660 0.340
#> TCGA-06-0195-01B-01 4 0.0188 0.9607 0.004 0.000 0.000 0.996
#> TCGA-06-0208-01B-01 4 0.3123 0.8069 0.000 0.000 0.156 0.844
#> TCGA-06-0214-01A-02 4 0.0188 0.9602 0.000 0.004 0.000 0.996
#> TCGA-06-0219-01A-01 4 0.0188 0.9607 0.004 0.000 0.000 0.996
#> TCGA-06-0221-01A-01 4 0.0188 0.9607 0.004 0.000 0.000 0.996
#> TCGA-06-0237-01A-02 4 0.0188 0.9598 0.000 0.000 0.004 0.996
#> TCGA-06-0240-01A-02 4 0.0336 0.9604 0.008 0.000 0.000 0.992
#> TCGA-08-0349-01A-01 4 0.0188 0.9607 0.004 0.000 0.000 0.996
#> TCGA-08-0380-01A-01 4 0.0188 0.9602 0.000 0.004 0.000 0.996
#> TCGA-08-0386-01A-01 3 0.0592 0.9461 0.000 0.000 0.984 0.016
#> TCGA-08-0520-01A-01 4 0.0336 0.9579 0.000 0.000 0.008 0.992
#> TCGA-02-0007-01A-01 3 0.3311 0.7839 0.172 0.000 0.828 0.000
#> TCGA-02-0009-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-02-0016-01A-01 3 0.0188 0.9546 0.000 0.000 0.996 0.004
#> TCGA-02-0021-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-02-0023-01B-01 3 0.0469 0.9504 0.000 0.000 0.988 0.012
#> TCGA-02-0027-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-02-0038-01A-01 3 0.0188 0.9547 0.000 0.000 0.996 0.004
#> TCGA-02-0043-01A-01 3 0.1296 0.9335 0.028 0.004 0.964 0.004
#> TCGA-02-0070-01A-01 3 0.0188 0.9544 0.000 0.004 0.996 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.0188 0.9541 0.000 0.004 0.996 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-06-0137-01A-03 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-06-0148-01A-01 3 0.0336 0.9519 0.000 0.008 0.992 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-06-0402-01A-01 3 0.0804 0.9456 0.012 0.008 0.980 0.000
#> TCGA-08-0246-01A-01 3 0.0188 0.9547 0.000 0.000 0.996 0.004
#> TCGA-08-0354-01A-01 3 0.3157 0.8131 0.000 0.144 0.852 0.004
#> TCGA-08-0355-01A-01 3 0.0188 0.9547 0.000 0.000 0.996 0.004
#> TCGA-08-0357-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-08-0358-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-08-0375-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-08-0514-01A-01 3 0.0188 0.9547 0.000 0.000 0.996 0.004
#> TCGA-08-0518-01A-01 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.9564 0.000 0.000 1.000 0.000
#> TCGA-08-0531-01A-01 3 0.0188 0.9547 0.000 0.000 0.996 0.004
#> TCGA-02-0057-01A-01 4 0.3479 0.8198 0.000 0.012 0.148 0.840
#> TCGA-02-0004-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.0188 0.9545 0.000 0.996 0.000 0.004
#> TCGA-02-0025-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0817 0.9386 0.000 0.976 0.000 0.024
#> TCGA-02-0051-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.0188 0.9545 0.000 0.996 0.000 0.004
#> TCGA-02-0055-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0079-01A-03 2 0.0336 0.9517 0.000 0.992 0.000 0.008
#> TCGA-02-0085-01A-01 4 0.0469 0.9565 0.000 0.012 0.000 0.988
#> TCGA-02-0086-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0106-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0188 0.9545 0.000 0.996 0.000 0.004
#> TCGA-02-0111-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-02-0326-01A-01 4 0.4905 0.4461 0.004 0.000 0.364 0.632
#> TCGA-02-0337-01A-01 2 0.0188 0.9545 0.000 0.996 0.000 0.004
#> TCGA-06-0122-01A-01 2 0.4925 0.2965 0.000 0.572 0.428 0.000
#> TCGA-06-0124-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 2 0.1118 0.9269 0.000 0.964 0.036 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.3266 0.7869 0.000 0.832 0.168 0.000
#> TCGA-06-0152-01A-02 3 0.0188 0.9541 0.000 0.004 0.996 0.000
#> TCGA-06-0154-01A-02 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.2589 0.8449 0.000 0.884 0.000 0.116
#> TCGA-06-0189-01A-05 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.4992 0.0847 0.000 0.524 0.476 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0188 0.9545 0.000 0.996 0.000 0.004
#> TCGA-08-0346-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-08-0352-01A-01 2 0.4855 0.4795 0.000 0.644 0.352 0.004
#> TCGA-08-0360-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.0336 0.9517 0.000 0.992 0.000 0.008
#> TCGA-08-0392-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.0188 0.9545 0.000 0.996 0.000 0.004
#> TCGA-08-0510-01A-01 2 0.4992 0.1328 0.000 0.524 0.476 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.0000 0.9566 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.1956 0.8352 0.916 0.000 0.000 0.008 0.076
#> TCGA-02-0010-01A-01 1 0.2471 0.8366 0.864 0.000 0.000 0.000 0.136
#> TCGA-02-0011-01B-01 5 0.4306 -0.3845 0.492 0.000 0.000 0.000 0.508
#> TCGA-02-0014-01A-01 1 0.1121 0.8321 0.956 0.000 0.000 0.000 0.044
#> TCGA-02-0024-01B-01 1 0.2891 0.8288 0.824 0.000 0.000 0.000 0.176
#> TCGA-02-0026-01B-01 1 0.3424 0.7997 0.760 0.000 0.000 0.000 0.240
#> TCGA-02-0028-01A-01 1 0.0404 0.8166 0.988 0.000 0.000 0.000 0.012
#> TCGA-02-0046-01A-01 1 0.1908 0.8392 0.908 0.000 0.000 0.000 0.092
#> TCGA-02-0047-01A-01 5 0.3594 0.5159 0.172 0.004 0.000 0.020 0.804
#> TCGA-02-0048-01A-01 1 0.4726 0.4574 0.684 0.000 0.280 0.020 0.016
#> TCGA-02-0060-01A-01 5 0.1251 0.5350 0.036 0.000 0.000 0.008 0.956
#> TCGA-02-0069-01A-01 1 0.2280 0.8381 0.880 0.000 0.000 0.000 0.120
#> TCGA-02-0074-01A-01 1 0.3480 0.7950 0.752 0.000 0.000 0.000 0.248
#> TCGA-02-0080-01A-01 5 0.2179 0.5400 0.100 0.000 0.004 0.000 0.896
#> TCGA-02-0084-01A-03 5 0.5017 0.4679 0.028 0.060 0.004 0.164 0.744
#> TCGA-02-0087-01A-01 5 0.4118 0.4880 0.040 0.012 0.000 0.160 0.788
#> TCGA-02-0104-01A-01 1 0.1082 0.7976 0.964 0.000 0.000 0.008 0.028
#> TCGA-02-0114-01A-01 1 0.0290 0.8145 0.992 0.000 0.000 0.000 0.008
#> TCGA-02-0281-01A-01 1 0.1197 0.8337 0.952 0.000 0.000 0.000 0.048
#> TCGA-02-0321-01A-01 1 0.5638 0.6107 0.636 0.192 0.000 0.000 0.172
#> TCGA-02-0325-01A-01 5 0.6298 -0.2719 0.412 0.000 0.152 0.000 0.436
#> TCGA-02-0338-01A-01 1 0.0510 0.8217 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0339-01A-01 1 0.2929 0.8279 0.820 0.000 0.000 0.000 0.180
#> TCGA-02-0432-01A-02 5 0.1121 0.5380 0.044 0.000 0.000 0.000 0.956
#> TCGA-02-0439-01A-01 5 0.2069 0.5160 0.012 0.000 0.000 0.076 0.912
#> TCGA-02-0440-01A-01 1 0.3003 0.8249 0.812 0.000 0.000 0.000 0.188
#> TCGA-02-0446-01A-01 1 0.4552 0.6458 0.632 0.012 0.000 0.004 0.352
#> TCGA-06-0128-01A-01 5 0.5714 0.4499 0.212 0.000 0.000 0.164 0.624
#> TCGA-06-0129-01A-01 1 0.3727 0.8081 0.768 0.000 0.000 0.016 0.216
#> TCGA-06-0146-01A-01 1 0.4304 0.4101 0.516 0.000 0.000 0.000 0.484
#> TCGA-06-0156-01A-01 1 0.4260 0.7854 0.784 0.088 0.000 0.004 0.124
#> TCGA-06-0166-01A-01 1 0.1965 0.8320 0.924 0.024 0.000 0.000 0.052
#> TCGA-06-0174-01A-01 1 0.0510 0.8100 0.984 0.000 0.000 0.000 0.016
#> TCGA-06-0177-01A-01 1 0.3336 0.8068 0.772 0.000 0.000 0.000 0.228
#> TCGA-06-0238-01A-02 5 0.6327 0.0378 0.168 0.000 0.000 0.348 0.484
#> TCGA-06-0241-01A-02 1 0.0510 0.8104 0.984 0.000 0.000 0.000 0.016
#> TCGA-06-0410-01A-01 1 0.2535 0.7393 0.892 0.000 0.000 0.076 0.032
#> TCGA-06-0413-01A-01 1 0.2732 0.8327 0.840 0.000 0.000 0.000 0.160
#> TCGA-06-0414-01A-01 1 0.1851 0.8382 0.912 0.000 0.000 0.000 0.088
#> TCGA-06-0646-01A-01 2 0.5234 0.6332 0.096 0.680 0.000 0.220 0.004
#> TCGA-06-0648-01A-01 1 0.3661 0.7695 0.724 0.000 0.000 0.000 0.276
#> TCGA-08-0245-01A-01 1 0.0703 0.8052 0.976 0.000 0.000 0.000 0.024
#> TCGA-08-0344-01A-01 1 0.3424 0.7997 0.760 0.000 0.000 0.000 0.240
#> TCGA-08-0347-01A-01 5 0.3814 0.3450 0.276 0.004 0.000 0.000 0.720
#> TCGA-08-0348-01A-01 1 0.4138 0.6268 0.616 0.000 0.000 0.000 0.384
#> TCGA-08-0350-01A-01 1 0.4030 0.6787 0.648 0.000 0.000 0.000 0.352
#> TCGA-08-0353-01A-01 3 0.2966 0.7498 0.184 0.000 0.816 0.000 0.000
#> TCGA-08-0359-01A-01 5 0.1168 0.5324 0.032 0.000 0.000 0.008 0.960
#> TCGA-08-0385-01A-01 1 0.3274 0.8104 0.780 0.000 0.000 0.000 0.220
#> TCGA-08-0517-01A-01 1 0.0963 0.8209 0.964 0.000 0.000 0.000 0.036
#> TCGA-08-0524-01A-01 1 0.0290 0.8184 0.992 0.000 0.000 0.000 0.008
#> TCGA-12-0616-01A-01 1 0.1082 0.7976 0.964 0.000 0.000 0.008 0.028
#> TCGA-12-0618-01A-01 1 0.3561 0.7851 0.740 0.000 0.000 0.000 0.260
#> TCGA-02-0089-01A-01 4 0.4738 0.5151 0.000 0.004 0.012 0.564 0.420
#> TCGA-02-0113-01A-01 4 0.3635 0.4316 0.000 0.000 0.248 0.748 0.004
#> TCGA-02-0115-01A-01 5 0.4171 -0.2483 0.000 0.000 0.000 0.396 0.604
#> TCGA-02-0451-01A-01 4 0.4047 0.5846 0.000 0.004 0.000 0.676 0.320
#> TCGA-06-0132-01A-02 5 0.3983 -0.0951 0.000 0.000 0.000 0.340 0.660
#> TCGA-06-0133-01A-02 4 0.4182 0.5667 0.000 0.000 0.000 0.600 0.400
#> TCGA-06-0138-01A-02 4 0.4003 0.6075 0.000 0.008 0.000 0.704 0.288
#> TCGA-06-0160-01A-01 5 0.2773 0.3565 0.000 0.000 0.000 0.164 0.836
#> TCGA-06-0162-01A-01 4 0.3480 0.6355 0.000 0.000 0.000 0.752 0.248
#> TCGA-06-0167-01A-01 5 0.3143 0.2810 0.000 0.000 0.000 0.204 0.796
#> TCGA-06-0171-01A-02 4 0.3366 0.6327 0.000 0.004 0.000 0.784 0.212
#> TCGA-06-0173-01A-01 4 0.3702 0.5688 0.000 0.032 0.036 0.840 0.092
#> TCGA-06-0179-01A-02 5 0.4201 -0.2829 0.000 0.000 0.000 0.408 0.592
#> TCGA-06-0182-01A-01 4 0.3706 0.4679 0.004 0.000 0.184 0.792 0.020
#> TCGA-06-0185-01A-01 4 0.4815 0.4706 0.000 0.000 0.244 0.692 0.064
#> TCGA-06-0195-01B-01 4 0.4307 0.4557 0.000 0.000 0.000 0.504 0.496
#> TCGA-06-0208-01B-01 4 0.4199 0.5127 0.000 0.000 0.180 0.764 0.056
#> TCGA-06-0214-01A-02 4 0.4066 0.5801 0.000 0.004 0.000 0.672 0.324
#> TCGA-06-0219-01A-01 4 0.3336 0.5493 0.000 0.000 0.000 0.772 0.228
#> TCGA-06-0221-01A-01 4 0.4294 0.4742 0.000 0.000 0.000 0.532 0.468
#> TCGA-06-0237-01A-02 4 0.3132 0.6289 0.000 0.000 0.008 0.820 0.172
#> TCGA-06-0240-01A-02 5 0.4101 -0.1828 0.000 0.000 0.000 0.372 0.628
#> TCGA-08-0349-01A-01 4 0.3766 0.6203 0.000 0.004 0.000 0.728 0.268
#> TCGA-08-0380-01A-01 4 0.4264 0.5064 0.000 0.004 0.000 0.620 0.376
#> TCGA-08-0386-01A-01 3 0.4221 0.6626 0.000 0.000 0.732 0.236 0.032
#> TCGA-08-0520-01A-01 4 0.4497 0.5805 0.000 0.000 0.016 0.632 0.352
#> TCGA-02-0007-01A-01 3 0.3449 0.8047 0.024 0.000 0.812 0.164 0.000
#> TCGA-02-0009-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0021-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0023-01B-01 3 0.0290 0.9283 0.000 0.000 0.992 0.008 0.000
#> TCGA-02-0027-01A-01 3 0.2520 0.8472 0.004 0.012 0.888 0.000 0.096
#> TCGA-02-0038-01A-01 3 0.3816 0.6340 0.000 0.000 0.696 0.304 0.000
#> TCGA-02-0043-01A-01 3 0.0566 0.9246 0.012 0.000 0.984 0.004 0.000
#> TCGA-02-0070-01A-01 3 0.0162 0.9294 0.000 0.004 0.996 0.000 0.000
#> TCGA-02-0102-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0290-01A-01 3 0.1043 0.9162 0.000 0.000 0.960 0.040 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0422-01A-01 3 0.0162 0.9303 0.000 0.000 0.996 0.004 0.000
#> TCGA-02-0430-01A-01 3 0.0794 0.9228 0.000 0.000 0.972 0.028 0.000
#> TCGA-06-0125-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0145-01A-04 3 0.0609 0.9252 0.000 0.000 0.980 0.020 0.000
#> TCGA-06-0148-01A-01 3 0.0162 0.9297 0.000 0.000 0.996 0.004 0.000
#> TCGA-06-0187-01A-01 3 0.1121 0.9144 0.000 0.000 0.956 0.044 0.000
#> TCGA-06-0211-01B-01 3 0.3305 0.7597 0.000 0.000 0.776 0.224 0.000
#> TCGA-06-0402-01A-01 3 0.2690 0.8318 0.000 0.000 0.844 0.156 0.000
#> TCGA-08-0246-01A-01 3 0.0510 0.9274 0.000 0.000 0.984 0.016 0.000
#> TCGA-08-0354-01A-01 3 0.4074 0.5577 0.000 0.000 0.636 0.364 0.000
#> TCGA-08-0355-01A-01 3 0.1732 0.8789 0.000 0.000 0.920 0.080 0.000
#> TCGA-08-0357-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0358-01A-01 3 0.0404 0.9285 0.000 0.000 0.988 0.012 0.000
#> TCGA-08-0375-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.9310 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.0609 0.9262 0.000 0.000 0.980 0.020 0.000
#> TCGA-08-0531-01A-01 3 0.0510 0.9273 0.000 0.000 0.984 0.016 0.000
#> TCGA-02-0057-01A-01 5 0.6321 0.1575 0.000 0.168 0.020 0.216 0.596
#> TCGA-02-0004-01A-01 2 0.0404 0.9367 0.000 0.988 0.000 0.012 0.000
#> TCGA-02-0006-01B-01 2 0.0880 0.9297 0.000 0.968 0.000 0.032 0.000
#> TCGA-02-0025-01A-01 2 0.0162 0.9371 0.000 0.996 0.000 0.004 0.000
#> TCGA-02-0033-01A-01 2 0.0290 0.9368 0.000 0.992 0.000 0.008 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9370 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0955 0.9287 0.000 0.968 0.000 0.004 0.028
#> TCGA-02-0051-01A-01 2 0.2230 0.8745 0.000 0.884 0.000 0.116 0.000
#> TCGA-02-0054-01A-01 2 0.4150 0.4996 0.000 0.612 0.000 0.388 0.000
#> TCGA-02-0055-01A-01 2 0.0510 0.9356 0.000 0.984 0.000 0.016 0.000
#> TCGA-02-0059-01A-01 2 0.0510 0.9356 0.000 0.984 0.000 0.016 0.000
#> TCGA-02-0064-01A-01 2 0.0771 0.9329 0.000 0.976 0.000 0.020 0.004
#> TCGA-02-0075-01A-01 2 0.0290 0.9368 0.000 0.992 0.000 0.008 0.000
#> TCGA-02-0079-01A-03 2 0.1310 0.9264 0.000 0.956 0.000 0.024 0.020
#> TCGA-02-0085-01A-01 5 0.5003 0.1009 0.000 0.424 0.000 0.032 0.544
#> TCGA-02-0086-01A-01 2 0.2561 0.8455 0.000 0.856 0.000 0.144 0.000
#> TCGA-02-0099-01A-01 2 0.0290 0.9372 0.000 0.992 0.000 0.008 0.000
#> TCGA-02-0106-01A-01 2 0.3662 0.7262 0.000 0.744 0.000 0.252 0.004
#> TCGA-02-0107-01A-01 2 0.0880 0.9302 0.000 0.968 0.000 0.032 0.000
#> TCGA-02-0111-01A-01 2 0.0290 0.9362 0.000 0.992 0.000 0.008 0.000
#> TCGA-02-0326-01A-01 5 0.4547 0.3842 0.012 0.024 0.200 0.012 0.752
#> TCGA-02-0337-01A-01 2 0.1018 0.9312 0.000 0.968 0.000 0.016 0.016
#> TCGA-06-0122-01A-01 2 0.3184 0.8588 0.000 0.868 0.068 0.052 0.012
#> TCGA-06-0124-01A-01 2 0.0290 0.9368 0.000 0.992 0.000 0.008 0.000
#> TCGA-06-0130-01A-01 2 0.0290 0.9374 0.000 0.992 0.000 0.008 0.000
#> TCGA-06-0139-01A-01 2 0.0404 0.9355 0.000 0.988 0.000 0.012 0.000
#> TCGA-06-0143-01A-01 2 0.1648 0.9179 0.000 0.940 0.000 0.040 0.020
#> TCGA-06-0147-01A-01 2 0.0510 0.9344 0.000 0.984 0.000 0.016 0.000
#> TCGA-06-0149-01A-05 2 0.6224 0.4048 0.000 0.568 0.196 0.232 0.004
#> TCGA-06-0152-01A-02 3 0.1831 0.8857 0.000 0.004 0.920 0.076 0.000
#> TCGA-06-0154-01A-02 2 0.0579 0.9357 0.000 0.984 0.008 0.008 0.000
#> TCGA-06-0164-01A-01 2 0.0162 0.9371 0.000 0.996 0.000 0.004 0.000
#> TCGA-06-0175-01A-01 2 0.0703 0.9335 0.000 0.976 0.000 0.024 0.000
#> TCGA-06-0176-01A-03 2 0.0609 0.9349 0.000 0.980 0.000 0.020 0.000
#> TCGA-06-0184-01A-01 4 0.4718 0.0772 0.000 0.444 0.000 0.540 0.016
#> TCGA-06-0189-01A-05 2 0.0290 0.9371 0.000 0.992 0.000 0.008 0.000
#> TCGA-06-0190-01A-01 2 0.0290 0.9368 0.000 0.992 0.000 0.008 0.000
#> TCGA-06-0194-01A-01 2 0.0404 0.9374 0.000 0.988 0.000 0.012 0.000
#> TCGA-06-0197-01A-02 2 0.0404 0.9369 0.000 0.988 0.000 0.012 0.000
#> TCGA-06-0210-01A-01 2 0.0510 0.9373 0.000 0.984 0.000 0.016 0.000
#> TCGA-06-0397-01A-01 2 0.0703 0.9337 0.000 0.976 0.000 0.024 0.000
#> TCGA-06-0409-01A-02 2 0.0880 0.9298 0.000 0.968 0.000 0.032 0.000
#> TCGA-06-0412-01A-01 3 0.3389 0.7972 0.000 0.116 0.836 0.048 0.000
#> TCGA-06-0644-01A-02 2 0.0880 0.9308 0.000 0.968 0.000 0.032 0.000
#> TCGA-06-0645-01A-01 2 0.2068 0.8886 0.000 0.904 0.000 0.092 0.004
#> TCGA-08-0346-01A-01 2 0.0162 0.9370 0.000 0.996 0.000 0.004 0.000
#> TCGA-08-0352-01A-01 2 0.0613 0.9360 0.000 0.984 0.008 0.004 0.004
#> TCGA-08-0360-01A-01 2 0.1205 0.9242 0.000 0.956 0.000 0.040 0.004
#> TCGA-08-0390-01A-01 2 0.3934 0.6435 0.000 0.740 0.000 0.244 0.016
#> TCGA-08-0392-01A-01 2 0.3835 0.7113 0.000 0.732 0.000 0.260 0.008
#> TCGA-08-0509-01A-01 2 0.1671 0.9035 0.000 0.924 0.000 0.076 0.000
#> TCGA-08-0510-01A-01 3 0.4238 0.4113 0.000 0.368 0.628 0.000 0.004
#> TCGA-08-0512-01A-01 2 0.0290 0.9368 0.000 0.992 0.000 0.008 0.000
#> TCGA-08-0522-01A-01 2 0.0404 0.9365 0.000 0.988 0.000 0.012 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9370 0.000 1.000 0.000 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.2728 0.8677 0.000 0.888 0.068 0.040 0.004
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.3174 0.7508 0.840 0.000 0.000 0.012 0.040 0.108
#> TCGA-02-0010-01A-01 1 0.0725 0.7932 0.976 0.000 0.000 0.000 0.012 0.012
#> TCGA-02-0011-01B-01 1 0.5315 0.3428 0.596 0.000 0.000 0.000 0.224 0.180
#> TCGA-02-0014-01A-01 1 0.0622 0.7946 0.980 0.000 0.000 0.000 0.012 0.008
#> TCGA-02-0024-01B-01 1 0.2448 0.7903 0.884 0.000 0.000 0.000 0.052 0.064
#> TCGA-02-0026-01B-01 1 0.2277 0.7689 0.892 0.000 0.000 0.000 0.032 0.076
#> TCGA-02-0028-01A-01 1 0.1390 0.7910 0.948 0.000 0.004 0.000 0.032 0.016
#> TCGA-02-0046-01A-01 1 0.0993 0.7951 0.964 0.000 0.000 0.000 0.012 0.024
#> TCGA-02-0047-01A-01 5 0.6123 0.3566 0.240 0.000 0.000 0.004 0.412 0.344
#> TCGA-02-0048-01A-01 1 0.5702 0.4001 0.644 0.000 0.220 0.072 0.044 0.020
#> TCGA-02-0060-01A-01 6 0.1429 0.5186 0.052 0.000 0.000 0.004 0.004 0.940
#> TCGA-02-0069-01A-01 1 0.0993 0.7924 0.964 0.000 0.000 0.000 0.012 0.024
#> TCGA-02-0074-01A-01 1 0.3295 0.6998 0.816 0.000 0.000 0.000 0.128 0.056
#> TCGA-02-0080-01A-01 6 0.6305 -0.2732 0.256 0.000 0.012 0.000 0.312 0.420
#> TCGA-02-0084-01A-03 5 0.6106 0.5043 0.124 0.048 0.004 0.080 0.668 0.076
#> TCGA-02-0087-01A-01 5 0.6477 0.4922 0.168 0.000 0.008 0.072 0.568 0.184
#> TCGA-02-0104-01A-01 1 0.3066 0.7324 0.832 0.000 0.000 0.000 0.124 0.044
#> TCGA-02-0114-01A-01 1 0.1865 0.7813 0.920 0.000 0.000 0.000 0.040 0.040
#> TCGA-02-0281-01A-01 1 0.1003 0.7947 0.964 0.000 0.000 0.000 0.020 0.016
#> TCGA-02-0321-01A-01 1 0.6721 -0.0907 0.420 0.304 0.004 0.004 0.244 0.024
#> TCGA-02-0325-01A-01 5 0.6800 0.2734 0.372 0.000 0.100 0.000 0.408 0.120
#> TCGA-02-0338-01A-01 1 0.1970 0.7782 0.900 0.000 0.000 0.000 0.092 0.008
#> TCGA-02-0339-01A-01 1 0.1594 0.7887 0.932 0.000 0.000 0.000 0.016 0.052
#> TCGA-02-0432-01A-02 6 0.5667 -0.1361 0.192 0.000 0.000 0.000 0.288 0.520
#> TCGA-02-0439-01A-01 5 0.6589 0.1936 0.132 0.000 0.012 0.040 0.412 0.404
#> TCGA-02-0440-01A-01 1 0.1434 0.7850 0.940 0.000 0.000 0.000 0.012 0.048
#> TCGA-02-0446-01A-01 1 0.5282 0.5189 0.676 0.128 0.000 0.000 0.040 0.156
#> TCGA-06-0128-01A-01 1 0.6791 -0.2292 0.420 0.000 0.000 0.148 0.352 0.080
#> TCGA-06-0129-01A-01 1 0.3835 0.6069 0.748 0.000 0.000 0.000 0.204 0.048
#> TCGA-06-0146-01A-01 1 0.5364 0.2693 0.572 0.000 0.000 0.000 0.276 0.152
#> TCGA-06-0156-01A-01 1 0.2975 0.7414 0.840 0.000 0.000 0.016 0.132 0.012
#> TCGA-06-0166-01A-01 1 0.3291 0.7585 0.848 0.060 0.000 0.000 0.036 0.056
#> TCGA-06-0174-01A-01 1 0.2420 0.7654 0.884 0.000 0.000 0.000 0.076 0.040
#> TCGA-06-0177-01A-01 1 0.1757 0.7775 0.916 0.000 0.000 0.000 0.008 0.076
#> TCGA-06-0238-01A-02 6 0.5477 0.2830 0.264 0.000 0.000 0.156 0.004 0.576
#> TCGA-06-0241-01A-02 1 0.2129 0.7750 0.904 0.000 0.000 0.000 0.056 0.040
#> TCGA-06-0410-01A-01 1 0.3755 0.7075 0.800 0.000 0.000 0.024 0.132 0.044
#> TCGA-06-0413-01A-01 1 0.1434 0.7899 0.940 0.000 0.000 0.000 0.012 0.048
#> TCGA-06-0414-01A-01 1 0.1575 0.7952 0.936 0.000 0.000 0.000 0.032 0.032
#> TCGA-06-0646-01A-01 5 0.6859 0.3819 0.144 0.128 0.000 0.232 0.496 0.000
#> TCGA-06-0648-01A-01 1 0.2662 0.7491 0.856 0.000 0.000 0.000 0.024 0.120
#> TCGA-08-0245-01A-01 1 0.2775 0.7484 0.856 0.000 0.000 0.000 0.104 0.040
#> TCGA-08-0344-01A-01 1 0.2402 0.7552 0.868 0.000 0.000 0.000 0.012 0.120
#> TCGA-08-0347-01A-01 5 0.5937 0.4370 0.308 0.004 0.000 0.000 0.480 0.208
#> TCGA-08-0348-01A-01 1 0.4681 0.4879 0.668 0.000 0.000 0.000 0.232 0.100
#> TCGA-08-0350-01A-01 1 0.5121 0.2593 0.568 0.000 0.000 0.000 0.332 0.100
#> TCGA-08-0353-01A-01 3 0.3860 0.6248 0.236 0.000 0.728 0.036 0.000 0.000
#> TCGA-08-0359-01A-01 6 0.5183 0.0549 0.116 0.000 0.000 0.004 0.272 0.608
#> TCGA-08-0385-01A-01 1 0.2282 0.7661 0.888 0.000 0.000 0.000 0.024 0.088
#> TCGA-08-0517-01A-01 1 0.1480 0.7903 0.940 0.000 0.000 0.000 0.020 0.040
#> TCGA-08-0524-01A-01 1 0.2537 0.7588 0.872 0.000 0.000 0.000 0.096 0.032
#> TCGA-12-0616-01A-01 1 0.3207 0.7343 0.828 0.000 0.000 0.004 0.124 0.044
#> TCGA-12-0618-01A-01 1 0.2771 0.7448 0.852 0.000 0.000 0.000 0.032 0.116
#> TCGA-02-0089-01A-01 4 0.4664 0.4934 0.000 0.000 0.000 0.644 0.076 0.280
#> TCGA-02-0113-01A-01 4 0.3900 0.5707 0.000 0.004 0.196 0.760 0.032 0.008
#> TCGA-02-0115-01A-01 6 0.2994 0.5346 0.000 0.000 0.004 0.208 0.000 0.788
#> TCGA-02-0451-01A-01 4 0.2937 0.6442 0.000 0.000 0.000 0.848 0.056 0.096
#> TCGA-06-0132-01A-02 6 0.2668 0.5770 0.000 0.000 0.000 0.168 0.004 0.828
#> TCGA-06-0133-01A-02 4 0.2562 0.6418 0.000 0.000 0.000 0.828 0.000 0.172
#> TCGA-06-0138-01A-02 4 0.2258 0.6619 0.000 0.000 0.000 0.896 0.060 0.044
#> TCGA-06-0160-01A-01 6 0.1812 0.5828 0.008 0.000 0.000 0.080 0.000 0.912
#> TCGA-06-0162-01A-01 4 0.2398 0.6624 0.000 0.000 0.000 0.876 0.020 0.104
#> TCGA-06-0167-01A-01 6 0.1858 0.5876 0.004 0.000 0.000 0.092 0.000 0.904
#> TCGA-06-0171-01A-02 4 0.1501 0.6770 0.000 0.000 0.000 0.924 0.000 0.076
#> TCGA-06-0173-01A-01 4 0.3011 0.6629 0.000 0.008 0.012 0.852 0.016 0.112
#> TCGA-06-0179-01A-02 6 0.2762 0.5514 0.000 0.000 0.000 0.196 0.000 0.804
#> TCGA-06-0182-01A-01 4 0.3262 0.6542 0.008 0.000 0.072 0.852 0.052 0.016
#> TCGA-06-0185-01A-01 4 0.3394 0.5460 0.000 0.000 0.236 0.752 0.000 0.012
#> TCGA-06-0195-01B-01 6 0.3851 -0.0543 0.000 0.000 0.000 0.460 0.000 0.540
#> TCGA-06-0208-01B-01 4 0.3047 0.6675 0.000 0.000 0.080 0.852 0.008 0.060
#> TCGA-06-0214-01A-02 4 0.3424 0.6258 0.000 0.000 0.000 0.812 0.092 0.096
#> TCGA-06-0219-01A-01 4 0.3221 0.6041 0.000 0.000 0.000 0.792 0.020 0.188
#> TCGA-06-0221-01A-01 4 0.3620 0.4098 0.000 0.000 0.000 0.648 0.000 0.352
#> TCGA-06-0237-01A-02 4 0.0779 0.6800 0.000 0.000 0.008 0.976 0.008 0.008
#> TCGA-06-0240-01A-02 6 0.2597 0.5716 0.000 0.000 0.000 0.176 0.000 0.824
#> TCGA-08-0349-01A-01 4 0.2758 0.6636 0.000 0.000 0.012 0.872 0.080 0.036
#> TCGA-08-0380-01A-01 4 0.4200 0.5130 0.000 0.000 0.000 0.720 0.208 0.072
#> TCGA-08-0386-01A-01 3 0.6285 -0.0268 0.000 0.000 0.424 0.420 0.080 0.076
#> TCGA-08-0520-01A-01 4 0.3939 0.6371 0.000 0.000 0.020 0.784 0.056 0.140
#> TCGA-02-0007-01A-01 3 0.6760 0.3012 0.028 0.008 0.500 0.308 0.128 0.028
#> TCGA-02-0009-01A-01 3 0.1036 0.8892 0.000 0.000 0.964 0.024 0.008 0.004
#> TCGA-02-0016-01A-01 3 0.1382 0.8888 0.000 0.000 0.948 0.036 0.008 0.008
#> TCGA-02-0021-01A-01 3 0.1152 0.8862 0.000 0.000 0.952 0.044 0.000 0.004
#> TCGA-02-0023-01B-01 3 0.2742 0.8551 0.000 0.000 0.872 0.044 0.076 0.008
#> TCGA-02-0027-01A-01 3 0.2419 0.8378 0.016 0.028 0.896 0.000 0.000 0.060
#> TCGA-02-0038-01A-01 4 0.3727 0.2957 0.000 0.000 0.388 0.612 0.000 0.000
#> TCGA-02-0043-01A-01 3 0.1498 0.8837 0.012 0.000 0.948 0.012 0.024 0.004
#> TCGA-02-0070-01A-01 3 0.1615 0.8607 0.000 0.004 0.928 0.000 0.064 0.004
#> TCGA-02-0102-01A-01 3 0.0692 0.8848 0.000 0.000 0.976 0.000 0.020 0.004
#> TCGA-02-0260-01A-03 3 0.0777 0.8879 0.000 0.000 0.972 0.000 0.024 0.004
#> TCGA-02-0269-01B-01 3 0.1010 0.8868 0.000 0.000 0.960 0.004 0.036 0.000
#> TCGA-02-0285-01A-01 3 0.1074 0.8898 0.000 0.000 0.960 0.012 0.028 0.000
#> TCGA-02-0289-01A-01 3 0.0935 0.8882 0.000 0.000 0.964 0.004 0.032 0.000
#> TCGA-02-0290-01A-01 3 0.1794 0.8878 0.000 0.000 0.924 0.036 0.040 0.000
#> TCGA-02-0317-01A-01 3 0.1196 0.8875 0.000 0.000 0.952 0.008 0.040 0.000
#> TCGA-02-0333-01A-02 3 0.1267 0.8812 0.000 0.000 0.940 0.000 0.060 0.000
#> TCGA-02-0422-01A-01 3 0.1391 0.8870 0.000 0.000 0.944 0.040 0.016 0.000
#> TCGA-02-0430-01A-01 3 0.1141 0.8847 0.000 0.000 0.948 0.052 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0508 0.8853 0.000 0.000 0.984 0.000 0.012 0.004
#> TCGA-06-0126-01A-01 3 0.0436 0.8872 0.000 0.000 0.988 0.004 0.004 0.004
#> TCGA-06-0137-01A-03 3 0.0520 0.8859 0.000 0.000 0.984 0.000 0.008 0.008
#> TCGA-06-0145-01A-04 3 0.1531 0.8811 0.000 0.000 0.928 0.068 0.000 0.004
#> TCGA-06-0148-01A-01 3 0.0935 0.8826 0.000 0.000 0.964 0.000 0.032 0.004
#> TCGA-06-0187-01A-01 3 0.1908 0.8656 0.000 0.000 0.900 0.096 0.004 0.000
#> TCGA-06-0211-01B-01 3 0.2980 0.7759 0.000 0.000 0.808 0.180 0.012 0.000
#> TCGA-06-0402-01A-01 3 0.2751 0.8664 0.008 0.008 0.888 0.056 0.032 0.008
#> TCGA-08-0246-01A-01 3 0.1528 0.8893 0.000 0.000 0.936 0.048 0.016 0.000
#> TCGA-08-0354-01A-01 4 0.5173 -0.0418 0.000 0.000 0.452 0.476 0.064 0.008
#> TCGA-08-0355-01A-01 3 0.4657 0.6575 0.000 0.000 0.688 0.176 0.136 0.000
#> TCGA-08-0357-01A-01 3 0.1480 0.8865 0.000 0.000 0.940 0.040 0.020 0.000
#> TCGA-08-0358-01A-01 3 0.2856 0.8519 0.000 0.000 0.856 0.068 0.076 0.000
#> TCGA-08-0375-01A-01 3 0.1418 0.8885 0.000 0.000 0.944 0.032 0.024 0.000
#> TCGA-08-0511-01A-01 3 0.0363 0.8856 0.000 0.000 0.988 0.000 0.012 0.000
#> TCGA-08-0514-01A-01 3 0.0547 0.8850 0.000 0.000 0.980 0.000 0.020 0.000
#> TCGA-08-0518-01A-01 3 0.0603 0.8853 0.000 0.000 0.980 0.000 0.016 0.004
#> TCGA-08-0529-01A-02 3 0.1471 0.8813 0.000 0.000 0.932 0.064 0.004 0.000
#> TCGA-08-0531-01A-01 3 0.1082 0.8874 0.000 0.000 0.956 0.040 0.004 0.000
#> TCGA-02-0057-01A-01 5 0.6486 0.3735 0.000 0.104 0.044 0.144 0.620 0.088
#> TCGA-02-0004-01A-01 2 0.0508 0.8409 0.000 0.984 0.000 0.000 0.012 0.004
#> TCGA-02-0006-01B-01 2 0.4094 0.6884 0.000 0.652 0.000 0.024 0.324 0.000
#> TCGA-02-0025-01A-01 2 0.0713 0.8443 0.000 0.972 0.000 0.000 0.028 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.8413 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.1501 0.8410 0.000 0.924 0.000 0.000 0.076 0.000
#> TCGA-02-0039-01A-01 2 0.3705 0.7919 0.000 0.776 0.000 0.008 0.180 0.036
#> TCGA-02-0051-01A-01 2 0.2322 0.8009 0.000 0.896 0.000 0.024 0.072 0.008
#> TCGA-02-0054-01A-01 4 0.5101 0.0741 0.000 0.424 0.000 0.504 0.068 0.004
#> TCGA-02-0055-01A-01 2 0.0632 0.8370 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-02-0059-01A-01 2 0.0260 0.8403 0.000 0.992 0.000 0.000 0.008 0.000
#> TCGA-02-0064-01A-01 2 0.3575 0.7402 0.000 0.708 0.000 0.008 0.284 0.000
#> TCGA-02-0075-01A-01 2 0.1908 0.8387 0.000 0.916 0.028 0.000 0.056 0.000
#> TCGA-02-0079-01A-03 2 0.4135 0.5932 0.000 0.584 0.000 0.008 0.404 0.004
#> TCGA-02-0085-01A-01 6 0.4664 0.1830 0.000 0.324 0.000 0.020 0.028 0.628
#> TCGA-02-0086-01A-01 2 0.1908 0.8285 0.000 0.924 0.012 0.020 0.044 0.000
#> TCGA-02-0099-01A-01 2 0.2420 0.8290 0.000 0.864 0.000 0.004 0.128 0.004
#> TCGA-02-0106-01A-01 2 0.2658 0.7879 0.000 0.876 0.000 0.036 0.080 0.008
#> TCGA-02-0107-01A-01 2 0.3898 0.7159 0.000 0.684 0.000 0.020 0.296 0.000
#> TCGA-02-0111-01A-01 2 0.1910 0.8335 0.000 0.892 0.000 0.000 0.108 0.000
#> TCGA-02-0326-01A-01 6 0.6052 0.1771 0.024 0.016 0.096 0.008 0.268 0.588
#> TCGA-02-0337-01A-01 2 0.4696 0.5861 0.012 0.580 0.000 0.008 0.384 0.016
#> TCGA-06-0122-01A-01 2 0.5974 0.4270 0.000 0.484 0.244 0.004 0.268 0.000
#> TCGA-06-0124-01A-01 2 0.2618 0.8316 0.000 0.872 0.052 0.000 0.076 0.000
#> TCGA-06-0130-01A-01 2 0.0363 0.8425 0.000 0.988 0.000 0.000 0.012 0.000
#> TCGA-06-0139-01A-01 2 0.2597 0.8094 0.000 0.824 0.000 0.000 0.176 0.000
#> TCGA-06-0143-01A-01 2 0.4672 0.5119 0.000 0.532 0.028 0.000 0.432 0.008
#> TCGA-06-0147-01A-01 2 0.2996 0.7807 0.000 0.772 0.000 0.000 0.228 0.000
#> TCGA-06-0149-01A-05 5 0.6090 0.0688 0.000 0.056 0.084 0.388 0.472 0.000
#> TCGA-06-0152-01A-02 3 0.6019 0.1696 0.000 0.004 0.464 0.300 0.232 0.000
#> TCGA-06-0154-01A-02 2 0.2471 0.8268 0.000 0.888 0.052 0.004 0.056 0.000
#> TCGA-06-0164-01A-01 2 0.1267 0.8455 0.000 0.940 0.000 0.000 0.060 0.000
#> TCGA-06-0175-01A-01 2 0.4081 0.7652 0.000 0.772 0.092 0.012 0.124 0.000
#> TCGA-06-0176-01A-03 2 0.0777 0.8361 0.000 0.972 0.000 0.000 0.024 0.004
#> TCGA-06-0184-01A-01 4 0.6308 0.0351 0.000 0.212 0.000 0.476 0.288 0.024
#> TCGA-06-0189-01A-05 2 0.0260 0.8419 0.000 0.992 0.000 0.000 0.008 0.000
#> TCGA-06-0190-01A-01 2 0.0632 0.8433 0.000 0.976 0.000 0.000 0.024 0.000
#> TCGA-06-0194-01A-01 2 0.0458 0.8439 0.000 0.984 0.000 0.000 0.016 0.000
#> TCGA-06-0197-01A-02 2 0.0858 0.8449 0.000 0.968 0.000 0.004 0.028 0.000
#> TCGA-06-0210-01A-01 2 0.3164 0.8214 0.000 0.824 0.032 0.004 0.140 0.000
#> TCGA-06-0397-01A-01 2 0.1442 0.8292 0.000 0.944 0.012 0.004 0.040 0.000
#> TCGA-06-0409-01A-02 2 0.3950 0.7287 0.000 0.696 0.000 0.028 0.276 0.000
#> TCGA-06-0412-01A-01 3 0.4531 0.7412 0.000 0.056 0.752 0.132 0.060 0.000
#> TCGA-06-0644-01A-02 2 0.1080 0.8326 0.000 0.960 0.000 0.004 0.032 0.004
#> TCGA-06-0645-01A-01 2 0.4635 0.6398 0.000 0.608 0.000 0.056 0.336 0.000
#> TCGA-08-0346-01A-01 2 0.1444 0.8415 0.000 0.928 0.000 0.000 0.072 0.000
#> TCGA-08-0352-01A-01 2 0.4552 0.6925 0.000 0.700 0.172 0.000 0.128 0.000
#> TCGA-08-0360-01A-01 2 0.3899 0.6636 0.000 0.628 0.000 0.008 0.364 0.000
#> TCGA-08-0390-01A-01 2 0.3286 0.7566 0.000 0.836 0.000 0.104 0.016 0.044
#> TCGA-08-0392-01A-01 2 0.3048 0.7631 0.000 0.848 0.000 0.044 0.100 0.008
#> TCGA-08-0509-01A-01 2 0.4637 0.6622 0.000 0.628 0.000 0.064 0.308 0.000
#> TCGA-08-0510-01A-01 3 0.4526 0.4832 0.000 0.244 0.676 0.000 0.080 0.000
#> TCGA-08-0512-01A-01 2 0.0260 0.8427 0.000 0.992 0.000 0.000 0.008 0.000
#> TCGA-08-0522-01A-01 2 0.0547 0.8381 0.000 0.980 0.000 0.000 0.020 0.000
#> TCGA-12-0619-01A-01 2 0.1327 0.8437 0.000 0.936 0.000 0.000 0.064 0.000
#> TCGA-12-0620-01A-01 2 0.4636 0.7189 0.000 0.672 0.048 0.016 0.264 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> MAD:NMF 168 2.23e-22 2
#> MAD:NMF 146 6.00e-51 3
#> MAD:NMF 165 3.97e-72 4
#> MAD:NMF 146 4.80e-78 5
#> MAD:NMF 140 3.01e-75 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "hclust"]
# you can also extract it by
# res = res_list["ATC:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.406 0.736 0.871 0.4216 0.556 0.556
#> 3 3 0.329 0.500 0.708 0.4598 0.710 0.512
#> 4 4 0.373 0.464 0.648 0.1446 0.794 0.493
#> 5 5 0.469 0.463 0.666 0.0830 0.873 0.585
#> 6 6 0.537 0.438 0.669 0.0332 0.951 0.794
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.1414 0.7913 0.980 0.020
#> TCGA-02-0010-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0672 0.7940 0.992 0.008
#> TCGA-02-0014-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0376 0.7948 0.996 0.004
#> TCGA-02-0028-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.1414 0.7913 0.980 0.020
#> TCGA-02-0047-01A-01 2 0.7219 0.7674 0.200 0.800
#> TCGA-02-0048-01A-01 1 0.1414 0.7913 0.980 0.020
#> TCGA-02-0060-01A-01 2 0.9996 0.0324 0.488 0.512
#> TCGA-02-0069-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0672 0.7940 0.992 0.008
#> TCGA-02-0084-01A-03 2 0.7602 0.7453 0.220 0.780
#> TCGA-02-0087-01A-01 2 0.7602 0.7453 0.220 0.780
#> TCGA-02-0104-01A-01 1 0.5519 0.7420 0.872 0.128
#> TCGA-02-0114-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-02-0321-01A-01 2 0.8144 0.6810 0.252 0.748
#> TCGA-02-0325-01A-01 1 0.7139 0.7022 0.804 0.196
#> TCGA-02-0338-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0672 0.7940 0.992 0.008
#> TCGA-02-0439-01A-01 2 0.9815 0.3213 0.420 0.580
#> TCGA-02-0440-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-02-0446-01A-01 2 0.6973 0.7793 0.188 0.812
#> TCGA-06-0128-01A-01 2 0.9491 0.4502 0.368 0.632
#> TCGA-06-0129-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0376 0.7948 0.996 0.004
#> TCGA-06-0156-01A-01 2 0.6973 0.7793 0.188 0.812
#> TCGA-06-0166-01A-01 2 0.7056 0.7754 0.192 0.808
#> TCGA-06-0174-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0376 0.7948 0.996 0.004
#> TCGA-06-0238-01A-02 2 0.8327 0.6657 0.264 0.736
#> TCGA-06-0241-01A-02 1 0.0000 0.7946 1.000 0.000
#> TCGA-06-0410-01A-01 2 0.9944 0.1247 0.456 0.544
#> TCGA-06-0413-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.7139 0.7721 0.196 0.804
#> TCGA-06-0648-01A-01 1 0.0376 0.7948 0.996 0.004
#> TCGA-08-0245-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0672 0.7940 0.992 0.008
#> TCGA-08-0347-01A-01 2 0.8555 0.6612 0.280 0.720
#> TCGA-08-0348-01A-01 2 0.9815 0.3213 0.420 0.580
#> TCGA-08-0350-01A-01 1 0.9754 0.4077 0.592 0.408
#> TCGA-08-0353-01A-01 1 0.9323 0.5309 0.652 0.348
#> TCGA-08-0359-01A-01 2 0.9815 0.3213 0.420 0.580
#> TCGA-08-0385-01A-01 1 0.9732 0.4194 0.596 0.404
#> TCGA-08-0517-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.7946 1.000 0.000
#> TCGA-12-0616-01A-01 2 0.9087 0.5525 0.324 0.676
#> TCGA-12-0618-01A-01 1 0.0376 0.7948 0.996 0.004
#> TCGA-02-0089-01A-01 2 0.3733 0.8581 0.072 0.928
#> TCGA-02-0113-01A-01 2 0.2603 0.8657 0.044 0.956
#> TCGA-02-0115-01A-01 2 0.2778 0.8653 0.048 0.952
#> TCGA-02-0451-01A-01 2 0.4815 0.8417 0.104 0.896
#> TCGA-06-0132-01A-02 2 0.0000 0.8605 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.1843 0.8660 0.028 0.972
#> TCGA-06-0138-01A-02 2 0.1843 0.8660 0.028 0.972
#> TCGA-06-0160-01A-01 1 0.8813 0.5618 0.700 0.300
#> TCGA-06-0162-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.8813 0.5618 0.700 0.300
#> TCGA-06-0171-01A-02 2 0.1843 0.8660 0.028 0.972
#> TCGA-06-0173-01A-01 2 0.7056 0.7764 0.192 0.808
#> TCGA-06-0179-01A-02 2 0.0000 0.8605 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.3879 0.8513 0.076 0.924
#> TCGA-06-0185-01A-01 2 0.4939 0.8383 0.108 0.892
#> TCGA-06-0195-01B-01 2 0.9358 0.4585 0.352 0.648
#> TCGA-06-0208-01B-01 2 0.3431 0.8581 0.064 0.936
#> TCGA-06-0214-01A-02 2 0.4815 0.8417 0.104 0.896
#> TCGA-06-0219-01A-01 2 0.0938 0.8632 0.012 0.988
#> TCGA-06-0221-01A-01 2 0.0938 0.8632 0.012 0.988
#> TCGA-06-0237-01A-02 2 0.1843 0.8660 0.028 0.972
#> TCGA-06-0240-01A-02 2 0.1184 0.8644 0.016 0.984
#> TCGA-08-0349-01A-01 2 0.7056 0.7776 0.192 0.808
#> TCGA-08-0380-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.9427 0.5071 0.640 0.360
#> TCGA-08-0520-01A-01 2 0.3584 0.8600 0.068 0.932
#> TCGA-02-0007-01A-01 1 0.8144 0.6534 0.748 0.252
#> TCGA-02-0009-01A-01 1 0.8861 0.5994 0.696 0.304
#> TCGA-02-0016-01A-01 1 0.9491 0.4912 0.632 0.368
#> TCGA-02-0021-01A-01 1 0.9661 0.4368 0.608 0.392
#> TCGA-02-0023-01B-01 2 0.2948 0.8645 0.052 0.948
#> TCGA-02-0027-01A-01 2 0.9977 0.0918 0.472 0.528
#> TCGA-02-0038-01A-01 2 0.6623 0.7940 0.172 0.828
#> TCGA-02-0043-01A-01 1 0.8861 0.5994 0.696 0.304
#> TCGA-02-0070-01A-01 2 0.9286 0.5284 0.344 0.656
#> TCGA-02-0102-01A-01 1 0.8861 0.5994 0.696 0.304
#> TCGA-02-0260-01A-03 1 0.9460 0.5047 0.636 0.364
#> TCGA-02-0269-01B-01 1 0.9460 0.5047 0.636 0.364
#> TCGA-02-0285-01A-01 2 0.9209 0.5468 0.336 0.664
#> TCGA-02-0289-01A-01 1 0.9491 0.4963 0.632 0.368
#> TCGA-02-0290-01A-01 2 0.3584 0.8598 0.068 0.932
#> TCGA-02-0317-01A-01 1 0.9993 0.1291 0.516 0.484
#> TCGA-02-0333-01A-02 1 0.9491 0.4963 0.632 0.368
#> TCGA-02-0422-01A-01 2 0.9044 0.5827 0.320 0.680
#> TCGA-02-0430-01A-01 2 0.9358 0.5076 0.352 0.648
#> TCGA-06-0125-01A-01 1 0.8861 0.5994 0.696 0.304
#> TCGA-06-0126-01A-01 1 0.8861 0.5994 0.696 0.304
#> TCGA-06-0137-01A-03 1 0.9922 0.2564 0.552 0.448
#> TCGA-06-0145-01A-04 2 0.7453 0.7613 0.212 0.788
#> TCGA-06-0148-01A-01 1 0.9993 0.1162 0.516 0.484
#> TCGA-06-0187-01A-01 2 0.7299 0.7644 0.204 0.796
#> TCGA-06-0211-01B-01 2 0.9323 0.4829 0.348 0.652
#> TCGA-06-0402-01A-01 1 0.9661 0.4368 0.608 0.392
#> TCGA-08-0246-01A-01 2 0.4690 0.8478 0.100 0.900
#> TCGA-08-0354-01A-01 2 0.2043 0.8656 0.032 0.968
#> TCGA-08-0355-01A-01 2 0.2948 0.8645 0.052 0.948
#> TCGA-08-0357-01A-01 2 0.8555 0.6612 0.280 0.720
#> TCGA-08-0358-01A-01 2 0.7674 0.7214 0.224 0.776
#> TCGA-08-0375-01A-01 1 0.9087 0.5699 0.676 0.324
#> TCGA-08-0511-01A-01 2 0.8016 0.7121 0.244 0.756
#> TCGA-08-0514-01A-01 2 0.7674 0.7405 0.224 0.776
#> TCGA-08-0518-01A-01 1 0.9896 0.2859 0.560 0.440
#> TCGA-08-0529-01A-02 2 0.9209 0.5468 0.336 0.664
#> TCGA-08-0531-01A-01 2 0.9209 0.5473 0.336 0.664
#> TCGA-02-0057-01A-01 2 0.3733 0.8578 0.072 0.928
#> TCGA-02-0004-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.3733 0.8578 0.072 0.928
#> TCGA-02-0025-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.1184 0.8646 0.016 0.984
#> TCGA-02-0039-01A-01 2 0.1414 0.8660 0.020 0.980
#> TCGA-02-0051-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.4298 0.8511 0.088 0.912
#> TCGA-02-0055-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.2948 0.8648 0.052 0.948
#> TCGA-02-0075-01A-01 2 0.2948 0.8648 0.052 0.948
#> TCGA-02-0079-01A-03 2 0.0672 0.8638 0.008 0.992
#> TCGA-02-0085-01A-01 2 0.2948 0.8647 0.052 0.948
#> TCGA-02-0086-01A-01 2 0.0672 0.8637 0.008 0.992
#> TCGA-02-0099-01A-01 2 0.5408 0.8301 0.124 0.876
#> TCGA-02-0106-01A-01 2 0.0938 0.8642 0.012 0.988
#> TCGA-02-0107-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.7299 0.7488 0.204 0.796
#> TCGA-02-0337-01A-01 2 0.1184 0.8646 0.016 0.984
#> TCGA-06-0122-01A-01 2 0.6438 0.8045 0.164 0.836
#> TCGA-06-0124-01A-01 2 0.3114 0.8640 0.056 0.944
#> TCGA-06-0130-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.6801 0.7902 0.180 0.820
#> TCGA-06-0147-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.2043 0.8678 0.032 0.968
#> TCGA-06-0152-01A-02 2 0.2948 0.8636 0.052 0.948
#> TCGA-06-0154-01A-02 2 0.1633 0.8660 0.024 0.976
#> TCGA-06-0164-01A-01 2 0.0672 0.8632 0.008 0.992
#> TCGA-06-0175-01A-01 2 0.2603 0.8659 0.044 0.956
#> TCGA-06-0176-01A-03 2 0.1414 0.8653 0.020 0.980
#> TCGA-06-0184-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.8605 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.1633 0.8660 0.024 0.976
#> TCGA-06-0194-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.8605 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.1633 0.8660 0.024 0.976
#> TCGA-06-0397-01A-01 2 0.2236 0.8661 0.036 0.964
#> TCGA-06-0409-01A-02 2 0.1184 0.8651 0.016 0.984
#> TCGA-06-0412-01A-01 2 0.1633 0.8660 0.024 0.976
#> TCGA-06-0644-01A-02 2 0.0000 0.8605 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.1184 0.8651 0.016 0.984
#> TCGA-08-0346-01A-01 2 0.1633 0.8660 0.024 0.976
#> TCGA-08-0352-01A-01 2 0.6343 0.8075 0.160 0.840
#> TCGA-08-0360-01A-01 2 0.1633 0.8660 0.024 0.976
#> TCGA-08-0390-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.1184 0.8651 0.016 0.984
#> TCGA-08-0510-01A-01 2 0.2948 0.8648 0.052 0.948
#> TCGA-08-0512-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8605 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.1414 0.8653 0.020 0.980
#> TCGA-12-0620-01A-01 2 0.2043 0.8656 0.032 0.968
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.2066 8.03e-01 0.940 0.000 0.060
#> TCGA-02-0010-01A-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.1643 8.10e-01 0.956 0.000 0.044
#> TCGA-02-0014-01A-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0592 8.20e-01 0.988 0.000 0.012
#> TCGA-02-0028-01A-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.2066 8.03e-01 0.940 0.000 0.060
#> TCGA-02-0047-01A-01 3 0.8173 2.05e-01 0.072 0.420 0.508
#> TCGA-02-0048-01A-01 1 0.2165 8.00e-01 0.936 0.000 0.064
#> TCGA-02-0060-01A-01 3 0.7987 4.10e-01 0.292 0.092 0.616
#> TCGA-02-0069-01A-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0424 8.20e-01 0.992 0.000 0.008
#> TCGA-02-0080-01A-01 1 0.1643 8.10e-01 0.956 0.000 0.044
#> TCGA-02-0084-01A-03 3 0.4342 5.08e-01 0.024 0.120 0.856
#> TCGA-02-0087-01A-01 3 0.4342 5.08e-01 0.024 0.120 0.856
#> TCGA-02-0104-01A-01 1 0.5216 6.40e-01 0.740 0.000 0.260
#> TCGA-02-0114-01A-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.6882 5.14e-01 0.096 0.172 0.732
#> TCGA-02-0325-01A-01 1 0.5919 5.78e-01 0.724 0.016 0.260
#> TCGA-02-0338-01A-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.1643 8.10e-01 0.956 0.000 0.044
#> TCGA-02-0439-01A-01 3 0.8187 5.24e-01 0.244 0.128 0.628
#> TCGA-02-0440-01A-01 1 0.1529 8.15e-01 0.960 0.000 0.040
#> TCGA-02-0446-01A-01 3 0.8100 1.97e-01 0.068 0.420 0.512
#> TCGA-06-0128-01A-01 3 0.9153 3.64e-01 0.176 0.300 0.524
#> TCGA-06-0129-01A-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0592 8.20e-01 0.988 0.000 0.012
#> TCGA-06-0156-01A-01 3 0.8100 1.97e-01 0.068 0.420 0.512
#> TCGA-06-0166-01A-01 3 0.8179 1.93e-01 0.072 0.424 0.504
#> TCGA-06-0174-01A-01 1 0.1529 8.15e-01 0.960 0.000 0.040
#> TCGA-06-0177-01A-01 1 0.1643 8.16e-01 0.956 0.000 0.044
#> TCGA-06-0238-01A-02 3 0.3572 4.94e-01 0.040 0.060 0.900
#> TCGA-06-0241-01A-02 1 0.1529 8.15e-01 0.960 0.000 0.040
#> TCGA-06-0410-01A-01 3 0.9758 2.92e-01 0.304 0.256 0.440
#> TCGA-06-0413-01A-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.1529 8.15e-01 0.960 0.000 0.040
#> TCGA-06-0646-01A-01 3 0.8140 2.47e-01 0.072 0.404 0.524
#> TCGA-06-0648-01A-01 1 0.1411 8.17e-01 0.964 0.000 0.036
#> TCGA-08-0245-01A-01 1 0.1529 8.15e-01 0.960 0.000 0.040
#> TCGA-08-0344-01A-01 1 0.1643 8.10e-01 0.956 0.000 0.044
#> TCGA-08-0347-01A-01 3 0.8698 4.64e-01 0.136 0.300 0.564
#> TCGA-08-0348-01A-01 3 0.8187 5.24e-01 0.244 0.128 0.628
#> TCGA-08-0350-01A-01 3 0.6925 -9.15e-02 0.452 0.016 0.532
#> TCGA-08-0353-01A-01 1 0.8347 8.44e-03 0.512 0.084 0.404
#> TCGA-08-0359-01A-01 3 0.8187 5.24e-01 0.244 0.128 0.628
#> TCGA-08-0385-01A-01 3 0.6936 -1.15e-01 0.460 0.016 0.524
#> TCGA-08-0517-01A-01 1 0.1529 8.15e-01 0.960 0.000 0.040
#> TCGA-08-0524-01A-01 1 0.0000 8.20e-01 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 3 0.4920 4.95e-01 0.108 0.052 0.840
#> TCGA-12-0618-01A-01 1 0.1411 8.17e-01 0.964 0.000 0.036
#> TCGA-02-0089-01A-01 2 0.6294 5.67e-01 0.020 0.692 0.288
#> TCGA-02-0113-01A-01 2 0.6247 4.93e-01 0.004 0.620 0.376
#> TCGA-02-0115-01A-01 2 0.6297 5.26e-01 0.008 0.640 0.352
#> TCGA-02-0451-01A-01 2 0.7043 3.29e-01 0.024 0.576 0.400
#> TCGA-06-0132-01A-02 2 0.5138 5.91e-01 0.000 0.748 0.252
#> TCGA-06-0133-01A-02 2 0.6008 4.69e-01 0.000 0.628 0.372
#> TCGA-06-0138-01A-02 2 0.6026 4.64e-01 0.000 0.624 0.376
#> TCGA-06-0160-01A-01 1 0.6813 3.12e-01 0.520 0.012 0.468
#> TCGA-06-0162-01A-01 2 0.5882 4.83e-01 0.000 0.652 0.348
#> TCGA-06-0167-01A-01 1 0.6813 3.12e-01 0.520 0.012 0.468
#> TCGA-06-0171-01A-02 2 0.6026 4.64e-01 0.000 0.624 0.376
#> TCGA-06-0173-01A-01 3 0.8316 2.07e-01 0.080 0.424 0.496
#> TCGA-06-0179-01A-02 2 0.5138 5.91e-01 0.000 0.748 0.252
#> TCGA-06-0182-01A-01 2 0.7192 4.17e-01 0.032 0.588 0.380
#> TCGA-06-0185-01A-01 2 0.7736 3.46e-01 0.052 0.548 0.400
#> TCGA-06-0195-01B-01 3 0.9550 2.20e-01 0.200 0.352 0.448
#> TCGA-06-0208-01B-01 2 0.6849 4.36e-01 0.020 0.600 0.380
#> TCGA-06-0214-01A-02 2 0.7043 3.29e-01 0.024 0.576 0.400
#> TCGA-06-0219-01A-01 2 0.6079 4.52e-01 0.000 0.612 0.388
#> TCGA-06-0221-01A-01 2 0.6079 4.52e-01 0.000 0.612 0.388
#> TCGA-06-0237-01A-02 2 0.6026 4.64e-01 0.000 0.624 0.376
#> TCGA-06-0240-01A-02 2 0.6095 4.47e-01 0.000 0.608 0.392
#> TCGA-08-0349-01A-01 3 0.7990 2.44e-01 0.064 0.404 0.532
#> TCGA-08-0380-01A-01 2 0.5138 5.98e-01 0.000 0.748 0.252
#> TCGA-08-0386-01A-01 1 0.8268 -9.17e-02 0.484 0.076 0.440
#> TCGA-08-0520-01A-01 3 0.5859 1.82e-01 0.000 0.344 0.656
#> TCGA-02-0007-01A-01 1 0.6952 3.19e-01 0.600 0.024 0.376
#> TCGA-02-0009-01A-01 1 0.6950 2.54e-01 0.572 0.020 0.408
#> TCGA-02-0016-01A-01 3 0.7248 6.76e-02 0.436 0.028 0.536
#> TCGA-02-0021-01A-01 3 0.8273 1.46e-01 0.448 0.076 0.476
#> TCGA-02-0023-01B-01 3 0.6079 1.10e-01 0.000 0.388 0.612
#> TCGA-02-0027-01A-01 3 0.8258 4.67e-01 0.284 0.112 0.604
#> TCGA-02-0038-01A-01 2 0.7990 -8.26e-03 0.060 0.488 0.452
#> TCGA-02-0043-01A-01 1 0.6950 2.54e-01 0.572 0.020 0.408
#> TCGA-02-0070-01A-01 3 0.9006 5.12e-01 0.188 0.256 0.556
#> TCGA-02-0102-01A-01 1 0.6950 2.54e-01 0.572 0.020 0.408
#> TCGA-02-0260-01A-03 3 0.6869 1.32e-02 0.424 0.016 0.560
#> TCGA-02-0269-01B-01 3 0.6869 1.32e-02 0.424 0.016 0.560
#> TCGA-02-0285-01A-01 3 0.8907 5.03e-01 0.168 0.272 0.560
#> TCGA-02-0289-01A-01 3 0.6859 2.56e-02 0.420 0.016 0.564
#> TCGA-02-0290-01A-01 3 0.5760 2.19e-01 0.000 0.328 0.672
#> TCGA-02-0317-01A-01 3 0.6880 2.96e-01 0.304 0.036 0.660
#> TCGA-02-0333-01A-02 3 0.6859 2.56e-02 0.420 0.016 0.564
#> TCGA-02-0422-01A-01 3 0.8797 4.96e-01 0.156 0.276 0.568
#> TCGA-02-0430-01A-01 3 0.9021 5.13e-01 0.184 0.264 0.552
#> TCGA-06-0125-01A-01 1 0.6950 2.54e-01 0.572 0.020 0.408
#> TCGA-06-0126-01A-01 1 0.6950 2.54e-01 0.572 0.020 0.408
#> TCGA-06-0137-01A-03 3 0.8324 3.39e-01 0.372 0.088 0.540
#> TCGA-06-0145-01A-04 3 0.8655 2.98e-01 0.108 0.380 0.512
#> TCGA-06-0148-01A-01 3 0.8906 4.01e-01 0.344 0.136 0.520
#> TCGA-06-0187-01A-01 3 0.8363 2.41e-01 0.084 0.412 0.504
#> TCGA-06-0211-01B-01 3 0.9451 2.96e-01 0.184 0.364 0.452
#> TCGA-06-0402-01A-01 3 0.8273 1.46e-01 0.448 0.076 0.476
#> TCGA-08-0246-01A-01 2 0.7169 1.67e-01 0.024 0.520 0.456
#> TCGA-08-0354-01A-01 3 0.6204 -2.21e-02 0.000 0.424 0.576
#> TCGA-08-0355-01A-01 3 0.6079 1.10e-01 0.000 0.388 0.612
#> TCGA-08-0357-01A-01 3 0.8698 4.64e-01 0.136 0.300 0.564
#> TCGA-08-0358-01A-01 3 0.3272 4.83e-01 0.016 0.080 0.904
#> TCGA-08-0375-01A-01 1 0.7138 2.00e-01 0.540 0.024 0.436
#> TCGA-08-0511-01A-01 3 0.8457 3.68e-01 0.100 0.356 0.544
#> TCGA-08-0514-01A-01 3 0.8457 2.90e-01 0.092 0.396 0.512
#> TCGA-08-0518-01A-01 3 0.8250 2.97e-01 0.392 0.080 0.528
#> TCGA-08-0529-01A-02 3 0.8907 5.03e-01 0.168 0.272 0.560
#> TCGA-08-0531-01A-01 3 0.9050 4.86e-01 0.168 0.296 0.536
#> TCGA-02-0057-01A-01 2 0.6758 4.62e-01 0.020 0.620 0.360
#> TCGA-02-0004-01A-01 2 0.0237 6.92e-01 0.000 0.996 0.004
#> TCGA-02-0006-01B-01 2 0.6758 4.62e-01 0.020 0.620 0.360
#> TCGA-02-0025-01A-01 2 0.2066 6.93e-01 0.000 0.940 0.060
#> TCGA-02-0033-01A-01 2 0.0892 6.99e-01 0.000 0.980 0.020
#> TCGA-02-0034-01A-01 2 0.4968 6.72e-01 0.012 0.800 0.188
#> TCGA-02-0039-01A-01 2 0.5268 6.70e-01 0.012 0.776 0.212
#> TCGA-02-0051-01A-01 2 0.1643 6.91e-01 0.000 0.956 0.044
#> TCGA-02-0054-01A-01 2 0.7067 4.05e-01 0.028 0.596 0.376
#> TCGA-02-0055-01A-01 2 0.0592 6.93e-01 0.000 0.988 0.012
#> TCGA-02-0059-01A-01 2 0.0592 6.91e-01 0.000 0.988 0.012
#> TCGA-02-0064-01A-01 2 0.6326 5.51e-01 0.020 0.688 0.292
#> TCGA-02-0075-01A-01 2 0.6326 5.51e-01 0.020 0.688 0.292
#> TCGA-02-0079-01A-03 2 0.3340 6.85e-01 0.000 0.880 0.120
#> TCGA-02-0085-01A-01 2 0.6161 5.94e-01 0.016 0.696 0.288
#> TCGA-02-0086-01A-01 2 0.2496 7.04e-01 0.004 0.928 0.068
#> TCGA-02-0099-01A-01 2 0.7446 2.17e-01 0.036 0.532 0.432
#> TCGA-02-0106-01A-01 2 0.4291 6.96e-01 0.008 0.840 0.152
#> TCGA-02-0107-01A-01 2 0.0000 6.91e-01 0.000 1.000 0.000
#> TCGA-02-0111-01A-01 2 0.0592 6.91e-01 0.000 0.988 0.012
#> TCGA-02-0326-01A-01 3 0.2945 4.70e-01 0.004 0.088 0.908
#> TCGA-02-0337-01A-01 2 0.5020 6.71e-01 0.012 0.796 0.192
#> TCGA-06-0122-01A-01 2 0.7918 -7.45e-05 0.056 0.484 0.460
#> TCGA-06-0124-01A-01 2 0.6416 5.35e-01 0.020 0.676 0.304
#> TCGA-06-0130-01A-01 2 0.0892 6.99e-01 0.000 0.980 0.020
#> TCGA-06-0139-01A-01 2 0.0000 6.91e-01 0.000 1.000 0.000
#> TCGA-06-0143-01A-01 3 0.8179 1.97e-01 0.072 0.424 0.504
#> TCGA-06-0147-01A-01 2 0.0892 6.99e-01 0.000 0.980 0.020
#> TCGA-06-0149-01A-05 2 0.5737 6.33e-01 0.012 0.732 0.256
#> TCGA-06-0152-01A-02 3 0.6008 1.33e-01 0.000 0.372 0.628
#> TCGA-06-0154-01A-02 2 0.5020 6.71e-01 0.012 0.796 0.192
#> TCGA-06-0164-01A-01 2 0.1989 7.04e-01 0.004 0.948 0.048
#> TCGA-06-0175-01A-01 2 0.6027 5.86e-01 0.016 0.712 0.272
#> TCGA-06-0176-01A-03 2 0.4915 6.79e-01 0.012 0.804 0.184
#> TCGA-06-0184-01A-01 2 0.1753 7.00e-01 0.000 0.952 0.048
#> TCGA-06-0189-01A-05 2 0.0592 6.91e-01 0.000 0.988 0.012
#> TCGA-06-0190-01A-01 2 0.5020 6.71e-01 0.012 0.796 0.192
#> TCGA-06-0194-01A-01 2 0.1289 7.01e-01 0.000 0.968 0.032
#> TCGA-06-0197-01A-02 2 0.0592 6.91e-01 0.000 0.988 0.012
#> TCGA-06-0210-01A-01 2 0.5020 6.71e-01 0.012 0.796 0.192
#> TCGA-06-0397-01A-01 2 0.5315 6.56e-01 0.012 0.772 0.216
#> TCGA-06-0409-01A-02 2 0.4353 6.79e-01 0.008 0.836 0.156
#> TCGA-06-0412-01A-01 2 0.5020 6.71e-01 0.012 0.796 0.192
#> TCGA-06-0644-01A-02 2 0.0237 6.92e-01 0.000 0.996 0.004
#> TCGA-06-0645-01A-01 2 0.4099 6.86e-01 0.008 0.852 0.140
#> TCGA-08-0346-01A-01 2 0.4805 6.74e-01 0.012 0.812 0.176
#> TCGA-08-0352-01A-01 3 0.8203 1.41e-01 0.072 0.444 0.484
#> TCGA-08-0360-01A-01 2 0.4749 6.74e-01 0.012 0.816 0.172
#> TCGA-08-0390-01A-01 2 0.0892 6.89e-01 0.000 0.980 0.020
#> TCGA-08-0392-01A-01 2 0.1643 6.91e-01 0.000 0.956 0.044
#> TCGA-08-0509-01A-01 2 0.4353 6.79e-01 0.008 0.836 0.156
#> TCGA-08-0510-01A-01 2 0.6326 5.51e-01 0.020 0.688 0.292
#> TCGA-08-0512-01A-01 2 0.3340 7.01e-01 0.000 0.880 0.120
#> TCGA-08-0522-01A-01 2 0.1163 7.00e-01 0.000 0.972 0.028
#> TCGA-12-0619-01A-01 2 0.4915 6.79e-01 0.012 0.804 0.184
#> TCGA-12-0620-01A-01 3 0.6215 -2.98e-02 0.000 0.428 0.572
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.2760 0.8074 0.872 0.000 0.128 0.000
#> TCGA-02-0010-01A-01 1 0.0592 0.8629 0.984 0.000 0.000 0.016
#> TCGA-02-0011-01B-01 1 0.2021 0.8504 0.936 0.000 0.024 0.040
#> TCGA-02-0014-01A-01 1 0.0592 0.8629 0.984 0.000 0.000 0.016
#> TCGA-02-0024-01B-01 1 0.0592 0.8629 0.984 0.000 0.000 0.016
#> TCGA-02-0026-01B-01 1 0.1042 0.8620 0.972 0.000 0.008 0.020
#> TCGA-02-0028-01A-01 1 0.0592 0.8629 0.984 0.000 0.000 0.016
#> TCGA-02-0046-01A-01 1 0.2760 0.8074 0.872 0.000 0.128 0.000
#> TCGA-02-0047-01A-01 3 0.6788 0.3470 0.012 0.288 0.604 0.096
#> TCGA-02-0048-01A-01 1 0.2868 0.7998 0.864 0.000 0.136 0.000
#> TCGA-02-0060-01A-01 3 0.8070 0.2037 0.204 0.028 0.508 0.260
#> TCGA-02-0069-01A-01 1 0.0592 0.8629 0.984 0.000 0.000 0.016
#> TCGA-02-0074-01A-01 1 0.1297 0.8609 0.964 0.000 0.020 0.016
#> TCGA-02-0080-01A-01 1 0.2021 0.8504 0.936 0.000 0.024 0.040
#> TCGA-02-0084-01A-03 3 0.5564 -0.0810 0.000 0.020 0.544 0.436
#> TCGA-02-0087-01A-01 3 0.5564 -0.0810 0.000 0.020 0.544 0.436
#> TCGA-02-0104-01A-01 1 0.6327 0.6222 0.648 0.000 0.124 0.228
#> TCGA-02-0114-01A-01 1 0.0779 0.8633 0.980 0.000 0.004 0.016
#> TCGA-02-0281-01A-01 1 0.0592 0.8629 0.984 0.000 0.000 0.016
#> TCGA-02-0321-01A-01 4 0.8156 0.2259 0.060 0.104 0.384 0.452
#> TCGA-02-0325-01A-01 1 0.6296 0.5434 0.652 0.000 0.224 0.124
#> TCGA-02-0338-01A-01 1 0.0592 0.8629 0.984 0.000 0.000 0.016
#> TCGA-02-0339-01A-01 1 0.0592 0.8629 0.984 0.000 0.000 0.016
#> TCGA-02-0432-01A-02 1 0.2021 0.8504 0.936 0.000 0.024 0.040
#> TCGA-02-0439-01A-01 3 0.8131 0.2302 0.164 0.052 0.540 0.244
#> TCGA-02-0440-01A-01 1 0.2469 0.8265 0.892 0.000 0.108 0.000
#> TCGA-02-0446-01A-01 3 0.6445 0.3401 0.008 0.288 0.624 0.080
#> TCGA-06-0128-01A-01 4 0.9410 0.1806 0.124 0.184 0.336 0.356
#> TCGA-06-0129-01A-01 1 0.0592 0.8629 0.984 0.000 0.000 0.016
#> TCGA-06-0146-01A-01 1 0.0927 0.8624 0.976 0.000 0.008 0.016
#> TCGA-06-0156-01A-01 3 0.6445 0.3401 0.008 0.288 0.624 0.080
#> TCGA-06-0166-01A-01 3 0.6623 0.3406 0.012 0.288 0.616 0.084
#> TCGA-06-0174-01A-01 1 0.2469 0.8265 0.892 0.000 0.108 0.000
#> TCGA-06-0177-01A-01 1 0.2282 0.8494 0.924 0.000 0.052 0.024
#> TCGA-06-0238-01A-02 4 0.4936 0.3126 0.000 0.008 0.340 0.652
#> TCGA-06-0241-01A-02 1 0.2469 0.8265 0.892 0.000 0.108 0.000
#> TCGA-06-0410-01A-01 4 0.9549 0.2776 0.252 0.148 0.208 0.392
#> TCGA-06-0413-01A-01 1 0.0592 0.8629 0.984 0.000 0.000 0.016
#> TCGA-06-0414-01A-01 1 0.2469 0.8265 0.892 0.000 0.108 0.000
#> TCGA-06-0646-01A-01 3 0.6588 0.3646 0.012 0.272 0.628 0.088
#> TCGA-06-0648-01A-01 1 0.2002 0.8545 0.936 0.000 0.044 0.020
#> TCGA-08-0245-01A-01 1 0.2469 0.8265 0.892 0.000 0.108 0.000
#> TCGA-08-0344-01A-01 1 0.2111 0.8501 0.932 0.000 0.024 0.044
#> TCGA-08-0347-01A-01 3 0.7012 0.4592 0.056 0.192 0.660 0.092
#> TCGA-08-0348-01A-01 3 0.8131 0.2302 0.164 0.052 0.540 0.244
#> TCGA-08-0350-01A-01 1 0.7863 0.1328 0.380 0.000 0.276 0.344
#> TCGA-08-0353-01A-01 3 0.6635 0.3296 0.368 0.040 0.564 0.028
#> TCGA-08-0359-01A-01 3 0.8131 0.2302 0.164 0.052 0.540 0.244
#> TCGA-08-0385-01A-01 1 0.7850 0.1502 0.388 0.000 0.272 0.340
#> TCGA-08-0517-01A-01 1 0.2589 0.8214 0.884 0.000 0.116 0.000
#> TCGA-08-0524-01A-01 1 0.0592 0.8629 0.984 0.000 0.000 0.016
#> TCGA-12-0616-01A-01 4 0.6374 0.2403 0.056 0.008 0.356 0.580
#> TCGA-12-0618-01A-01 1 0.2002 0.8545 0.936 0.000 0.044 0.020
#> TCGA-02-0089-01A-01 2 0.7363 0.3075 0.000 0.476 0.356 0.168
#> TCGA-02-0113-01A-01 4 0.7661 0.2840 0.000 0.376 0.212 0.412
#> TCGA-02-0115-01A-01 2 0.7723 -0.1415 0.000 0.420 0.232 0.348
#> TCGA-02-0451-01A-01 3 0.6895 -0.0363 0.004 0.412 0.492 0.092
#> TCGA-06-0132-01A-02 2 0.5602 -0.3034 0.000 0.508 0.020 0.472
#> TCGA-06-0133-01A-02 4 0.6474 0.4814 0.000 0.388 0.076 0.536
#> TCGA-06-0138-01A-02 4 0.6464 0.4839 0.000 0.384 0.076 0.540
#> TCGA-06-0160-01A-01 1 0.7423 0.3208 0.476 0.000 0.180 0.344
#> TCGA-06-0162-01A-01 4 0.5453 0.4649 0.000 0.388 0.020 0.592
#> TCGA-06-0167-01A-01 1 0.7423 0.3208 0.476 0.000 0.180 0.344
#> TCGA-06-0171-01A-02 4 0.6464 0.4839 0.000 0.384 0.076 0.540
#> TCGA-06-0173-01A-01 3 0.6629 0.3540 0.016 0.280 0.624 0.080
#> TCGA-06-0179-01A-02 2 0.5602 -0.3034 0.000 0.508 0.020 0.472
#> TCGA-06-0182-01A-01 4 0.7305 0.4901 0.016 0.352 0.108 0.524
#> TCGA-06-0185-01A-01 4 0.8120 0.4512 0.032 0.328 0.164 0.476
#> TCGA-06-0195-01B-01 4 0.9362 0.3970 0.148 0.212 0.204 0.436
#> TCGA-06-0208-01B-01 4 0.7177 0.4878 0.012 0.360 0.104 0.524
#> TCGA-06-0214-01A-02 3 0.6895 -0.0363 0.004 0.412 0.492 0.092
#> TCGA-06-0219-01A-01 4 0.5403 0.4995 0.000 0.348 0.024 0.628
#> TCGA-06-0221-01A-01 4 0.5403 0.4995 0.000 0.348 0.024 0.628
#> TCGA-06-0237-01A-02 4 0.6464 0.4839 0.000 0.384 0.076 0.540
#> TCGA-06-0240-01A-02 4 0.5386 0.5013 0.000 0.344 0.024 0.632
#> TCGA-08-0349-01A-01 3 0.7879 0.2769 0.028 0.276 0.528 0.168
#> TCGA-08-0380-01A-01 2 0.5685 -0.2804 0.000 0.516 0.024 0.460
#> TCGA-08-0386-01A-01 3 0.6769 0.3514 0.360 0.044 0.564 0.032
#> TCGA-08-0520-01A-01 4 0.7421 0.5075 0.000 0.220 0.268 0.512
#> TCGA-02-0007-01A-01 3 0.6015 0.0920 0.452 0.004 0.512 0.032
#> TCGA-02-0009-01A-01 3 0.5708 0.1867 0.416 0.000 0.556 0.028
#> TCGA-02-0016-01A-01 3 0.6517 0.3317 0.288 0.000 0.604 0.108
#> TCGA-02-0021-01A-01 3 0.6267 0.4184 0.300 0.036 0.636 0.028
#> TCGA-02-0023-01B-01 4 0.7576 0.4883 0.000 0.260 0.256 0.484
#> TCGA-02-0027-01A-01 3 0.7122 0.4074 0.168 0.044 0.652 0.136
#> TCGA-02-0038-01A-01 3 0.6623 0.2426 0.008 0.324 0.588 0.080
#> TCGA-02-0043-01A-01 3 0.5724 0.1706 0.424 0.000 0.548 0.028
#> TCGA-02-0070-01A-01 3 0.5827 0.4938 0.068 0.144 0.748 0.040
#> TCGA-02-0102-01A-01 3 0.5724 0.1706 0.424 0.000 0.548 0.028
#> TCGA-02-0260-01A-03 3 0.7643 0.1212 0.276 0.000 0.468 0.256
#> TCGA-02-0269-01B-01 3 0.7643 0.1212 0.276 0.000 0.468 0.256
#> TCGA-02-0285-01A-01 3 0.6950 0.4718 0.068 0.164 0.676 0.092
#> TCGA-02-0289-01A-01 3 0.7627 0.1312 0.272 0.000 0.472 0.256
#> TCGA-02-0290-01A-01 4 0.7442 0.4964 0.000 0.212 0.284 0.504
#> TCGA-02-0317-01A-01 3 0.7450 0.1220 0.164 0.004 0.496 0.336
#> TCGA-02-0333-01A-02 3 0.7627 0.1312 0.272 0.000 0.472 0.256
#> TCGA-02-0422-01A-01 3 0.6570 0.4763 0.060 0.164 0.700 0.076
#> TCGA-02-0430-01A-01 3 0.7252 0.4739 0.080 0.164 0.656 0.100
#> TCGA-06-0125-01A-01 3 0.5708 0.1867 0.416 0.000 0.556 0.028
#> TCGA-06-0126-01A-01 3 0.5708 0.1867 0.416 0.000 0.556 0.028
#> TCGA-06-0137-01A-03 3 0.6109 0.4776 0.216 0.044 0.700 0.040
#> TCGA-06-0145-01A-04 3 0.5879 0.3708 0.048 0.248 0.688 0.016
#> TCGA-06-0148-01A-01 3 0.6509 0.4795 0.188 0.076 0.692 0.044
#> TCGA-06-0187-01A-01 3 0.6247 0.3638 0.024 0.272 0.656 0.048
#> TCGA-06-0211-01B-01 3 0.9343 -0.2040 0.096 0.228 0.344 0.332
#> TCGA-06-0402-01A-01 3 0.6267 0.4184 0.300 0.036 0.636 0.028
#> TCGA-08-0246-01A-01 3 0.7491 0.0635 0.004 0.352 0.480 0.164
#> TCGA-08-0354-01A-01 4 0.7483 0.5258 0.000 0.288 0.216 0.496
#> TCGA-08-0355-01A-01 4 0.7576 0.4883 0.000 0.260 0.256 0.484
#> TCGA-08-0357-01A-01 3 0.7012 0.4592 0.056 0.192 0.660 0.092
#> TCGA-08-0358-01A-01 4 0.5355 0.3198 0.000 0.020 0.360 0.620
#> TCGA-08-0375-01A-01 3 0.6621 0.1131 0.408 0.000 0.508 0.084
#> TCGA-08-0511-01A-01 3 0.6453 0.4305 0.036 0.232 0.672 0.060
#> TCGA-08-0514-01A-01 3 0.5982 0.3903 0.024 0.256 0.680 0.040
#> TCGA-08-0518-01A-01 3 0.6019 0.4748 0.236 0.040 0.692 0.032
#> TCGA-08-0529-01A-02 3 0.6950 0.4718 0.068 0.164 0.676 0.092
#> TCGA-08-0531-01A-01 3 0.7168 0.4751 0.080 0.192 0.652 0.076
#> TCGA-02-0057-01A-01 2 0.6148 0.2399 0.000 0.484 0.468 0.048
#> TCGA-02-0004-01A-01 2 0.1388 0.6113 0.000 0.960 0.012 0.028
#> TCGA-02-0006-01B-01 2 0.6148 0.2399 0.000 0.484 0.468 0.048
#> TCGA-02-0025-01A-01 2 0.3842 0.4983 0.000 0.836 0.036 0.128
#> TCGA-02-0033-01A-01 2 0.1209 0.6364 0.000 0.964 0.032 0.004
#> TCGA-02-0034-01A-01 2 0.4482 0.6409 0.000 0.728 0.264 0.008
#> TCGA-02-0039-01A-01 2 0.5900 0.6215 0.000 0.664 0.260 0.076
#> TCGA-02-0051-01A-01 2 0.4137 0.3937 0.000 0.780 0.012 0.208
#> TCGA-02-0054-01A-01 3 0.5931 -0.2108 0.000 0.460 0.504 0.036
#> TCGA-02-0055-01A-01 2 0.2714 0.5396 0.000 0.884 0.004 0.112
#> TCGA-02-0059-01A-01 2 0.2408 0.5465 0.000 0.896 0.000 0.104
#> TCGA-02-0064-01A-01 2 0.5310 0.4390 0.000 0.576 0.412 0.012
#> TCGA-02-0075-01A-01 2 0.5310 0.4390 0.000 0.576 0.412 0.012
#> TCGA-02-0079-01A-03 2 0.5279 0.2731 0.000 0.704 0.044 0.252
#> TCGA-02-0085-01A-01 2 0.5742 0.4904 0.000 0.596 0.368 0.036
#> TCGA-02-0086-01A-01 2 0.4482 0.5607 0.000 0.804 0.068 0.128
#> TCGA-02-0099-01A-01 3 0.5894 0.0174 0.000 0.392 0.568 0.040
#> TCGA-02-0106-01A-01 2 0.3945 0.6656 0.000 0.780 0.216 0.004
#> TCGA-02-0107-01A-01 2 0.1151 0.6105 0.000 0.968 0.008 0.024
#> TCGA-02-0111-01A-01 2 0.2408 0.5465 0.000 0.896 0.000 0.104
#> TCGA-02-0326-01A-01 4 0.5420 0.3301 0.000 0.024 0.352 0.624
#> TCGA-02-0337-01A-01 2 0.4567 0.6326 0.000 0.716 0.276 0.008
#> TCGA-06-0122-01A-01 3 0.5649 0.1660 0.016 0.352 0.620 0.012
#> TCGA-06-0124-01A-01 2 0.5345 0.4079 0.000 0.560 0.428 0.012
#> TCGA-06-0130-01A-01 2 0.1209 0.6364 0.000 0.964 0.032 0.004
#> TCGA-06-0139-01A-01 2 0.1151 0.6105 0.000 0.968 0.008 0.024
#> TCGA-06-0143-01A-01 3 0.5660 0.3012 0.024 0.292 0.668 0.016
#> TCGA-06-0147-01A-01 2 0.1209 0.6364 0.000 0.964 0.032 0.004
#> TCGA-06-0149-01A-05 2 0.6821 0.5192 0.000 0.592 0.256 0.152
#> TCGA-06-0152-01A-02 4 0.7299 0.5210 0.000 0.240 0.224 0.536
#> TCGA-06-0154-01A-02 2 0.4456 0.6307 0.000 0.716 0.280 0.004
#> TCGA-06-0164-01A-01 2 0.1940 0.6516 0.000 0.924 0.076 0.000
#> TCGA-06-0175-01A-01 2 0.5286 0.4956 0.004 0.604 0.384 0.008
#> TCGA-06-0176-01A-03 2 0.4372 0.6413 0.000 0.728 0.268 0.004
#> TCGA-06-0184-01A-01 2 0.3812 0.5244 0.000 0.832 0.028 0.140
#> TCGA-06-0189-01A-05 2 0.2408 0.5465 0.000 0.896 0.000 0.104
#> TCGA-06-0190-01A-01 2 0.4456 0.6307 0.000 0.716 0.280 0.004
#> TCGA-06-0194-01A-01 2 0.2586 0.6289 0.000 0.912 0.048 0.040
#> TCGA-06-0197-01A-02 2 0.2408 0.5465 0.000 0.896 0.000 0.104
#> TCGA-06-0210-01A-01 2 0.4456 0.6307 0.000 0.716 0.280 0.004
#> TCGA-06-0397-01A-01 2 0.4655 0.5982 0.000 0.684 0.312 0.004
#> TCGA-06-0409-01A-02 2 0.3688 0.6667 0.000 0.792 0.208 0.000
#> TCGA-06-0412-01A-01 2 0.4456 0.6307 0.000 0.716 0.280 0.004
#> TCGA-06-0644-01A-02 2 0.1388 0.6113 0.000 0.960 0.012 0.028
#> TCGA-06-0645-01A-01 2 0.3668 0.6674 0.000 0.808 0.188 0.004
#> TCGA-08-0346-01A-01 2 0.4155 0.6539 0.000 0.756 0.240 0.004
#> TCGA-08-0352-01A-01 3 0.6728 0.2478 0.024 0.308 0.604 0.064
#> TCGA-08-0360-01A-01 2 0.4122 0.6556 0.000 0.760 0.236 0.004
#> TCGA-08-0390-01A-01 2 0.2814 0.5141 0.000 0.868 0.000 0.132
#> TCGA-08-0392-01A-01 2 0.4137 0.3937 0.000 0.780 0.012 0.208
#> TCGA-08-0509-01A-01 2 0.3688 0.6667 0.000 0.792 0.208 0.000
#> TCGA-08-0510-01A-01 2 0.5310 0.4390 0.000 0.576 0.412 0.012
#> TCGA-08-0512-01A-01 2 0.3257 0.6663 0.000 0.844 0.152 0.004
#> TCGA-08-0522-01A-01 2 0.1398 0.6392 0.000 0.956 0.040 0.004
#> TCGA-12-0619-01A-01 2 0.4372 0.6413 0.000 0.728 0.268 0.004
#> TCGA-12-0620-01A-01 4 0.7517 0.5129 0.000 0.304 0.212 0.484
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.4247 0.74597 0.776 0.000 0.092 0.000 0.132
#> TCGA-02-0010-01A-01 1 0.0000 0.84509 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.2672 0.81740 0.896 0.000 0.016 0.024 0.064
#> TCGA-02-0014-01A-01 1 0.0000 0.84509 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.84509 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.1484 0.84227 0.944 0.000 0.008 0.000 0.048
#> TCGA-02-0028-01A-01 1 0.0000 0.84509 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.4247 0.74597 0.776 0.000 0.092 0.000 0.132
#> TCGA-02-0047-01A-01 3 0.5218 0.55622 0.004 0.120 0.740 0.108 0.028
#> TCGA-02-0048-01A-01 1 0.4478 0.72344 0.756 0.000 0.100 0.000 0.144
#> TCGA-02-0060-01A-01 5 0.7459 0.36257 0.116 0.000 0.364 0.092 0.428
#> TCGA-02-0069-01A-01 1 0.0000 0.84509 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0912 0.84345 0.972 0.000 0.012 0.000 0.016
#> TCGA-02-0080-01A-01 1 0.2672 0.81740 0.896 0.000 0.016 0.024 0.064
#> TCGA-02-0084-01A-03 5 0.6339 0.31770 0.000 0.004 0.352 0.148 0.496
#> TCGA-02-0087-01A-01 5 0.6339 0.31770 0.000 0.004 0.352 0.148 0.496
#> TCGA-02-0104-01A-01 1 0.7192 0.24951 0.468 0.004 0.052 0.124 0.352
#> TCGA-02-0114-01A-01 1 0.0771 0.84613 0.976 0.000 0.004 0.000 0.020
#> TCGA-02-0281-01A-01 1 0.0000 0.84509 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.7428 0.24173 0.004 0.056 0.192 0.252 0.496
#> TCGA-02-0325-01A-01 1 0.5541 0.30783 0.552 0.000 0.076 0.000 0.372
#> TCGA-02-0338-01A-01 1 0.0000 0.84509 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.84509 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.2672 0.81740 0.896 0.000 0.016 0.024 0.064
#> TCGA-02-0439-01A-01 3 0.7553 -0.25353 0.100 0.008 0.448 0.092 0.352
#> TCGA-02-0440-01A-01 1 0.3906 0.77283 0.800 0.000 0.068 0.000 0.132
#> TCGA-02-0446-01A-01 3 0.4901 0.56428 0.004 0.124 0.756 0.100 0.016
#> TCGA-06-0128-01A-01 4 0.7920 0.04689 0.072 0.012 0.340 0.408 0.168
#> TCGA-06-0129-01A-01 1 0.0000 0.84509 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.1557 0.84207 0.940 0.000 0.008 0.000 0.052
#> TCGA-06-0156-01A-01 3 0.4901 0.56428 0.004 0.124 0.756 0.100 0.016
#> TCGA-06-0166-01A-01 3 0.4954 0.56003 0.004 0.120 0.752 0.108 0.016
#> TCGA-06-0174-01A-01 1 0.3906 0.77283 0.800 0.000 0.068 0.000 0.132
#> TCGA-06-0177-01A-01 1 0.3446 0.80607 0.840 0.000 0.036 0.008 0.116
#> TCGA-06-0238-01A-02 5 0.5806 0.28341 0.000 0.004 0.096 0.332 0.568
#> TCGA-06-0241-01A-02 1 0.3906 0.77283 0.800 0.000 0.068 0.000 0.132
#> TCGA-06-0410-01A-01 4 0.8372 0.12515 0.188 0.020 0.188 0.456 0.148
#> TCGA-06-0413-01A-01 1 0.0000 0.84509 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.3906 0.77283 0.800 0.000 0.068 0.000 0.132
#> TCGA-06-0646-01A-01 3 0.5280 0.55796 0.004 0.116 0.740 0.104 0.036
#> TCGA-06-0648-01A-01 1 0.3142 0.81787 0.856 0.000 0.032 0.004 0.108
#> TCGA-08-0245-01A-01 1 0.3906 0.77283 0.800 0.000 0.068 0.000 0.132
#> TCGA-08-0344-01A-01 1 0.2502 0.81743 0.904 0.000 0.012 0.024 0.060
#> TCGA-08-0347-01A-01 3 0.5539 0.51703 0.024 0.060 0.748 0.088 0.080
#> TCGA-08-0348-01A-01 3 0.7553 -0.25353 0.100 0.008 0.448 0.092 0.352
#> TCGA-08-0350-01A-01 5 0.6873 0.40956 0.288 0.004 0.072 0.084 0.552
#> TCGA-08-0353-01A-01 3 0.6761 0.12064 0.220 0.008 0.508 0.004 0.260
#> TCGA-08-0359-01A-01 3 0.7553 -0.25353 0.100 0.008 0.448 0.092 0.352
#> TCGA-08-0385-01A-01 5 0.6737 0.39823 0.292 0.004 0.064 0.080 0.560
#> TCGA-08-0517-01A-01 1 0.4054 0.76219 0.788 0.000 0.072 0.000 0.140
#> TCGA-08-0524-01A-01 1 0.0000 0.84509 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 5 0.6513 0.35924 0.024 0.004 0.124 0.280 0.568
#> TCGA-12-0618-01A-01 1 0.3142 0.81787 0.856 0.000 0.032 0.004 0.108
#> TCGA-02-0089-01A-01 3 0.6810 0.18380 0.000 0.232 0.460 0.300 0.008
#> TCGA-02-0113-01A-01 4 0.5482 0.50455 0.000 0.092 0.268 0.636 0.004
#> TCGA-02-0115-01A-01 4 0.6115 0.36552 0.000 0.136 0.308 0.552 0.004
#> TCGA-02-0451-01A-01 3 0.5547 0.43533 0.000 0.208 0.644 0.148 0.000
#> TCGA-06-0132-01A-02 4 0.3612 0.57248 0.000 0.228 0.008 0.764 0.000
#> TCGA-06-0133-01A-02 4 0.3622 0.62371 0.000 0.068 0.096 0.832 0.004
#> TCGA-06-0138-01A-02 4 0.3745 0.62473 0.000 0.068 0.096 0.828 0.008
#> TCGA-06-0160-01A-01 1 0.7946 -0.20266 0.352 0.000 0.092 0.204 0.352
#> TCGA-06-0162-01A-01 4 0.1965 0.59240 0.000 0.096 0.000 0.904 0.000
#> TCGA-06-0167-01A-01 5 0.7946 0.13018 0.352 0.000 0.092 0.204 0.352
#> TCGA-06-0171-01A-02 4 0.3745 0.62473 0.000 0.068 0.096 0.828 0.008
#> TCGA-06-0173-01A-01 3 0.4906 0.56683 0.004 0.120 0.756 0.104 0.016
#> TCGA-06-0179-01A-02 4 0.3612 0.57248 0.000 0.228 0.008 0.764 0.000
#> TCGA-06-0182-01A-01 4 0.4695 0.60180 0.004 0.048 0.136 0.776 0.036
#> TCGA-06-0185-01A-01 4 0.5747 0.55255 0.004 0.048 0.216 0.676 0.056
#> TCGA-06-0195-01B-01 4 0.7511 0.28537 0.084 0.020 0.184 0.560 0.152
#> TCGA-06-0208-01B-01 4 0.4251 0.60698 0.000 0.048 0.132 0.796 0.024
#> TCGA-06-0214-01A-02 3 0.5547 0.43533 0.000 0.208 0.644 0.148 0.000
#> TCGA-06-0219-01A-01 4 0.1341 0.58794 0.000 0.056 0.000 0.944 0.000
#> TCGA-06-0221-01A-01 4 0.1341 0.58794 0.000 0.056 0.000 0.944 0.000
#> TCGA-06-0237-01A-02 4 0.3745 0.62473 0.000 0.068 0.096 0.828 0.008
#> TCGA-06-0240-01A-02 4 0.1502 0.58707 0.000 0.056 0.000 0.940 0.004
#> TCGA-08-0349-01A-01 3 0.7359 0.38048 0.004 0.124 0.560 0.168 0.144
#> TCGA-08-0380-01A-01 4 0.4217 0.51685 0.000 0.280 0.012 0.704 0.004
#> TCGA-08-0386-01A-01 3 0.6586 0.14949 0.216 0.008 0.544 0.004 0.228
#> TCGA-08-0520-01A-01 4 0.7471 0.24033 0.000 0.096 0.112 0.420 0.372
#> TCGA-02-0007-01A-01 3 0.6718 -0.04285 0.272 0.000 0.420 0.000 0.308
#> TCGA-02-0009-01A-01 3 0.6608 0.03017 0.256 0.000 0.460 0.000 0.284
#> TCGA-02-0016-01A-01 5 0.6359 0.14896 0.140 0.000 0.416 0.004 0.440
#> TCGA-02-0021-01A-01 3 0.6230 0.19295 0.156 0.008 0.568 0.000 0.268
#> TCGA-02-0023-01B-01 4 0.7875 0.23814 0.000 0.164 0.104 0.376 0.356
#> TCGA-02-0027-01A-01 3 0.6636 0.11748 0.076 0.004 0.576 0.064 0.280
#> TCGA-02-0038-01A-01 3 0.4945 0.53464 0.000 0.144 0.732 0.116 0.008
#> TCGA-02-0043-01A-01 3 0.6636 0.02260 0.264 0.000 0.452 0.000 0.284
#> TCGA-02-0070-01A-01 3 0.3984 0.49517 0.000 0.044 0.804 0.012 0.140
#> TCGA-02-0102-01A-01 3 0.6634 0.02276 0.260 0.000 0.452 0.000 0.288
#> TCGA-02-0260-01A-03 5 0.4704 0.57172 0.112 0.000 0.152 0.000 0.736
#> TCGA-02-0269-01B-01 5 0.4704 0.57172 0.112 0.000 0.152 0.000 0.736
#> TCGA-02-0285-01A-01 3 0.5033 0.49259 0.012 0.032 0.768 0.100 0.088
#> TCGA-02-0289-01A-01 5 0.4696 0.57188 0.108 0.000 0.156 0.000 0.736
#> TCGA-02-0290-01A-01 4 0.7381 0.20870 0.000 0.100 0.096 0.404 0.400
#> TCGA-02-0317-01A-01 5 0.4231 0.53893 0.004 0.000 0.160 0.060 0.776
#> TCGA-02-0333-01A-02 5 0.4696 0.57188 0.108 0.000 0.156 0.000 0.736
#> TCGA-02-0422-01A-01 3 0.4588 0.50764 0.012 0.032 0.800 0.088 0.068
#> TCGA-02-0430-01A-01 3 0.5430 0.47814 0.016 0.032 0.740 0.096 0.116
#> TCGA-06-0125-01A-01 3 0.6608 0.03017 0.256 0.000 0.460 0.000 0.284
#> TCGA-06-0126-01A-01 3 0.6608 0.03017 0.256 0.000 0.460 0.000 0.284
#> TCGA-06-0137-01A-03 3 0.5467 0.26400 0.084 0.004 0.652 0.004 0.256
#> TCGA-06-0145-01A-04 3 0.3432 0.55504 0.024 0.096 0.856 0.008 0.016
#> TCGA-06-0148-01A-01 3 0.5126 0.28656 0.036 0.016 0.652 0.000 0.296
#> TCGA-06-0187-01A-01 3 0.3888 0.57124 0.000 0.112 0.816 0.064 0.008
#> TCGA-06-0211-01B-01 4 0.7277 0.16189 0.012 0.020 0.344 0.440 0.184
#> TCGA-06-0402-01A-01 3 0.6230 0.19295 0.156 0.008 0.568 0.000 0.268
#> TCGA-08-0246-01A-01 3 0.6956 0.37097 0.000 0.200 0.560 0.184 0.056
#> TCGA-08-0354-01A-01 4 0.7419 0.30360 0.000 0.164 0.060 0.436 0.340
#> TCGA-08-0355-01A-01 4 0.7875 0.23814 0.000 0.164 0.104 0.376 0.356
#> TCGA-08-0357-01A-01 3 0.5539 0.51703 0.024 0.060 0.748 0.088 0.080
#> TCGA-08-0358-01A-01 5 0.5865 0.28217 0.000 0.004 0.104 0.324 0.568
#> TCGA-08-0375-01A-01 5 0.6723 0.21585 0.260 0.000 0.332 0.000 0.408
#> TCGA-08-0511-01A-01 3 0.3797 0.56108 0.000 0.076 0.836 0.064 0.024
#> TCGA-08-0514-01A-01 3 0.3977 0.57382 0.000 0.100 0.820 0.060 0.020
#> TCGA-08-0518-01A-01 3 0.5482 0.24917 0.092 0.004 0.636 0.000 0.268
#> TCGA-08-0529-01A-02 3 0.5033 0.49259 0.012 0.032 0.768 0.100 0.088
#> TCGA-08-0531-01A-01 3 0.5124 0.51215 0.016 0.040 0.768 0.096 0.080
#> TCGA-02-0057-01A-01 3 0.5468 0.24681 0.000 0.332 0.600 0.060 0.008
#> TCGA-02-0004-01A-01 2 0.1408 0.64725 0.000 0.948 0.008 0.044 0.000
#> TCGA-02-0006-01B-01 3 0.5468 0.24681 0.000 0.332 0.600 0.060 0.008
#> TCGA-02-0025-01A-01 2 0.3650 0.51981 0.000 0.796 0.000 0.176 0.028
#> TCGA-02-0033-01A-01 2 0.1082 0.66610 0.000 0.964 0.028 0.008 0.000
#> TCGA-02-0034-01A-01 2 0.4553 0.48367 0.000 0.604 0.384 0.004 0.008
#> TCGA-02-0039-01A-01 2 0.6121 0.44203 0.000 0.536 0.352 0.100 0.012
#> TCGA-02-0051-01A-01 2 0.3796 0.33611 0.000 0.700 0.000 0.300 0.000
#> TCGA-02-0054-01A-01 3 0.5131 0.30725 0.000 0.296 0.648 0.048 0.008
#> TCGA-02-0055-01A-01 2 0.2561 0.57702 0.000 0.856 0.000 0.144 0.000
#> TCGA-02-0059-01A-01 2 0.2424 0.58881 0.000 0.868 0.000 0.132 0.000
#> TCGA-02-0064-01A-01 3 0.4745 -0.04407 0.000 0.424 0.560 0.004 0.012
#> TCGA-02-0075-01A-01 3 0.4745 -0.04407 0.000 0.424 0.560 0.004 0.012
#> TCGA-02-0079-01A-03 2 0.4880 0.19359 0.000 0.616 0.000 0.348 0.036
#> TCGA-02-0085-01A-01 3 0.5367 -0.16761 0.000 0.468 0.488 0.036 0.008
#> TCGA-02-0086-01A-01 2 0.5343 0.45891 0.000 0.656 0.088 0.252 0.004
#> TCGA-02-0099-01A-01 3 0.4690 0.41736 0.000 0.240 0.708 0.048 0.004
#> TCGA-02-0106-01A-01 2 0.3932 0.55229 0.000 0.672 0.328 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.1205 0.64660 0.000 0.956 0.004 0.040 0.000
#> TCGA-02-0111-01A-01 2 0.2424 0.58881 0.000 0.868 0.000 0.132 0.000
#> TCGA-02-0326-01A-01 5 0.5813 0.25236 0.000 0.000 0.112 0.328 0.560
#> TCGA-02-0337-01A-01 2 0.4585 0.46573 0.000 0.592 0.396 0.004 0.008
#> TCGA-06-0122-01A-01 3 0.3795 0.47898 0.000 0.184 0.788 0.004 0.024
#> TCGA-06-0124-01A-01 3 0.4714 0.00392 0.000 0.408 0.576 0.004 0.012
#> TCGA-06-0130-01A-01 2 0.1082 0.66610 0.000 0.964 0.028 0.008 0.000
#> TCGA-06-0139-01A-01 2 0.1205 0.64660 0.000 0.956 0.004 0.040 0.000
#> TCGA-06-0143-01A-01 3 0.3209 0.52963 0.000 0.120 0.848 0.004 0.028
#> TCGA-06-0147-01A-01 2 0.1082 0.66610 0.000 0.964 0.028 0.008 0.000
#> TCGA-06-0149-01A-05 2 0.7387 0.32574 0.000 0.432 0.320 0.204 0.044
#> TCGA-06-0152-01A-02 4 0.7174 0.23467 0.000 0.128 0.056 0.432 0.384
#> TCGA-06-0154-01A-02 2 0.4455 0.45425 0.000 0.588 0.404 0.000 0.008
#> TCGA-06-0164-01A-01 2 0.2818 0.66600 0.000 0.856 0.132 0.012 0.000
#> TCGA-06-0175-01A-01 3 0.4835 -0.16568 0.004 0.456 0.528 0.004 0.008
#> TCGA-06-0176-01A-03 2 0.4380 0.49260 0.000 0.616 0.376 0.000 0.008
#> TCGA-06-0184-01A-01 2 0.4495 0.47216 0.000 0.712 0.044 0.244 0.000
#> TCGA-06-0189-01A-05 2 0.2424 0.58881 0.000 0.868 0.000 0.132 0.000
#> TCGA-06-0190-01A-01 2 0.4455 0.45425 0.000 0.588 0.404 0.000 0.008
#> TCGA-06-0194-01A-01 2 0.3543 0.66836 0.000 0.828 0.112 0.060 0.000
#> TCGA-06-0197-01A-02 2 0.2424 0.58881 0.000 0.868 0.000 0.132 0.000
#> TCGA-06-0210-01A-01 2 0.4455 0.45425 0.000 0.588 0.404 0.000 0.008
#> TCGA-06-0397-01A-01 2 0.4528 0.36628 0.000 0.548 0.444 0.000 0.008
#> TCGA-06-0409-01A-02 2 0.4260 0.56694 0.000 0.680 0.308 0.008 0.004
#> TCGA-06-0412-01A-01 2 0.4455 0.45425 0.000 0.588 0.404 0.000 0.008
#> TCGA-06-0644-01A-02 2 0.1408 0.64725 0.000 0.948 0.008 0.044 0.000
#> TCGA-06-0645-01A-01 2 0.4380 0.58260 0.000 0.688 0.292 0.016 0.004
#> TCGA-08-0346-01A-01 2 0.4580 0.52423 0.000 0.628 0.356 0.008 0.008
#> TCGA-08-0352-01A-01 3 0.4920 0.50116 0.000 0.140 0.752 0.080 0.028
#> TCGA-08-0360-01A-01 2 0.4565 0.52855 0.000 0.632 0.352 0.008 0.008
#> TCGA-08-0390-01A-01 2 0.2929 0.53606 0.000 0.820 0.000 0.180 0.000
#> TCGA-08-0392-01A-01 2 0.3796 0.33611 0.000 0.700 0.000 0.300 0.000
#> TCGA-08-0509-01A-01 2 0.4260 0.56694 0.000 0.680 0.308 0.008 0.004
#> TCGA-08-0510-01A-01 3 0.4745 -0.04407 0.000 0.424 0.560 0.004 0.012
#> TCGA-08-0512-01A-01 2 0.2966 0.63566 0.000 0.816 0.184 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.1251 0.66802 0.000 0.956 0.036 0.008 0.000
#> TCGA-12-0619-01A-01 2 0.4380 0.49260 0.000 0.616 0.376 0.000 0.008
#> TCGA-12-0620-01A-01 4 0.7521 0.28874 0.000 0.192 0.056 0.412 0.340
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.4010 0.70011 0.764 0.000 0.084 0.000 0.004 0.148
#> TCGA-02-0010-01A-01 1 0.0000 0.81388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.3767 0.64533 0.720 0.000 0.004 0.000 0.016 0.260
#> TCGA-02-0014-01A-01 1 0.0000 0.81388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.81388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.2377 0.78222 0.868 0.000 0.004 0.000 0.004 0.124
#> TCGA-02-0028-01A-01 1 0.0000 0.81388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.4010 0.70011 0.764 0.000 0.084 0.000 0.004 0.148
#> TCGA-02-0047-01A-01 3 0.4912 0.56463 0.004 0.064 0.760 0.084 0.064 0.024
#> TCGA-02-0048-01A-01 1 0.4185 0.67379 0.744 0.000 0.084 0.000 0.004 0.168
#> TCGA-02-0060-01A-01 5 0.7237 0.16789 0.044 0.004 0.288 0.024 0.432 0.208
#> TCGA-02-0069-01A-01 1 0.0000 0.81388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0777 0.81021 0.972 0.000 0.004 0.000 0.000 0.024
#> TCGA-02-0080-01A-01 1 0.3767 0.64533 0.720 0.000 0.004 0.000 0.016 0.260
#> TCGA-02-0084-01A-03 5 0.4341 0.38447 0.000 0.004 0.272 0.036 0.684 0.004
#> TCGA-02-0087-01A-01 5 0.4341 0.38447 0.000 0.004 0.272 0.036 0.684 0.004
#> TCGA-02-0104-01A-01 6 0.5460 0.18585 0.128 0.008 0.000 0.036 0.156 0.672
#> TCGA-02-0114-01A-01 1 0.0858 0.81174 0.968 0.000 0.004 0.000 0.000 0.028
#> TCGA-02-0281-01A-01 1 0.0000 0.81388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.6976 0.44791 0.000 0.052 0.132 0.144 0.572 0.100
#> TCGA-02-0325-01A-01 1 0.6722 0.20193 0.480 0.000 0.068 0.000 0.200 0.252
#> TCGA-02-0338-01A-01 1 0.0146 0.81296 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-02-0339-01A-01 1 0.0146 0.81296 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-02-0432-01A-02 1 0.3767 0.64533 0.720 0.000 0.004 0.000 0.016 0.260
#> TCGA-02-0439-01A-01 5 0.7231 0.18292 0.040 0.012 0.368 0.024 0.400 0.156
#> TCGA-02-0440-01A-01 1 0.3691 0.72688 0.788 0.000 0.060 0.000 0.004 0.148
#> TCGA-02-0446-01A-01 3 0.4708 0.57422 0.004 0.072 0.776 0.072 0.048 0.028
#> TCGA-06-0128-01A-01 4 0.7979 0.11859 0.016 0.004 0.292 0.320 0.216 0.152
#> TCGA-06-0129-01A-01 1 0.0000 0.81388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.2420 0.78209 0.864 0.000 0.004 0.000 0.004 0.128
#> TCGA-06-0156-01A-01 3 0.4708 0.57422 0.004 0.072 0.776 0.072 0.048 0.028
#> TCGA-06-0166-01A-01 3 0.4628 0.57006 0.004 0.064 0.780 0.080 0.048 0.024
#> TCGA-06-0174-01A-01 1 0.3691 0.72688 0.788 0.000 0.060 0.000 0.004 0.148
#> TCGA-06-0177-01A-01 1 0.3861 0.72156 0.744 0.000 0.028 0.000 0.008 0.220
#> TCGA-06-0238-01A-02 5 0.5182 0.39733 0.000 0.004 0.024 0.156 0.684 0.132
#> TCGA-06-0241-01A-02 1 0.3691 0.72688 0.788 0.000 0.060 0.000 0.004 0.148
#> TCGA-06-0410-01A-01 4 0.8655 0.26696 0.132 0.008 0.140 0.380 0.180 0.160
#> TCGA-06-0413-01A-01 1 0.0000 0.81388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.3691 0.72688 0.788 0.000 0.060 0.000 0.004 0.148
#> TCGA-06-0646-01A-01 3 0.4907 0.56538 0.004 0.064 0.764 0.072 0.064 0.032
#> TCGA-06-0648-01A-01 1 0.3731 0.73505 0.756 0.000 0.024 0.000 0.008 0.212
#> TCGA-08-0245-01A-01 1 0.3691 0.72688 0.788 0.000 0.060 0.000 0.004 0.148
#> TCGA-08-0344-01A-01 1 0.3606 0.64752 0.728 0.000 0.000 0.000 0.016 0.256
#> TCGA-08-0347-01A-01 3 0.5741 0.51851 0.020 0.040 0.712 0.052 0.100 0.076
#> TCGA-08-0348-01A-01 5 0.7231 0.18292 0.040 0.012 0.368 0.024 0.400 0.156
#> TCGA-08-0350-01A-01 5 0.7034 0.08721 0.228 0.008 0.032 0.016 0.456 0.260
#> TCGA-08-0353-01A-01 3 0.6425 -0.10881 0.204 0.000 0.456 0.008 0.016 0.316
#> TCGA-08-0359-01A-01 5 0.7231 0.18292 0.040 0.012 0.368 0.024 0.400 0.156
#> TCGA-08-0385-01A-01 5 0.7073 0.07851 0.232 0.008 0.032 0.016 0.444 0.268
#> TCGA-08-0517-01A-01 1 0.3821 0.71396 0.776 0.000 0.064 0.000 0.004 0.156
#> TCGA-08-0524-01A-01 1 0.0000 0.81388 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 5 0.5777 0.38889 0.004 0.008 0.048 0.124 0.656 0.160
#> TCGA-12-0618-01A-01 1 0.3731 0.73505 0.756 0.000 0.024 0.000 0.008 0.212
#> TCGA-02-0089-01A-01 3 0.5831 0.19154 0.000 0.160 0.528 0.300 0.012 0.000
#> TCGA-02-0113-01A-01 4 0.4967 0.53539 0.000 0.036 0.296 0.636 0.028 0.004
#> TCGA-02-0115-01A-01 4 0.5425 0.41155 0.000 0.064 0.360 0.552 0.020 0.004
#> TCGA-02-0451-01A-01 3 0.4646 0.50504 0.000 0.128 0.728 0.128 0.012 0.004
#> TCGA-06-0132-01A-02 4 0.3718 0.58387 0.000 0.148 0.016 0.800 0.008 0.028
#> TCGA-06-0133-01A-02 4 0.2926 0.69083 0.000 0.012 0.112 0.852 0.024 0.000
#> TCGA-06-0138-01A-02 4 0.3078 0.69176 0.000 0.012 0.112 0.844 0.032 0.000
#> TCGA-06-0160-01A-01 6 0.5868 0.10200 0.044 0.004 0.016 0.032 0.420 0.484
#> TCGA-06-0162-01A-01 4 0.1592 0.63044 0.000 0.032 0.000 0.940 0.008 0.020
#> TCGA-06-0167-01A-01 6 0.5868 0.10200 0.044 0.004 0.016 0.032 0.420 0.484
#> TCGA-06-0171-01A-02 4 0.3078 0.69176 0.000 0.012 0.112 0.844 0.032 0.000
#> TCGA-06-0173-01A-01 3 0.4092 0.57600 0.000 0.056 0.812 0.068 0.036 0.028
#> TCGA-06-0179-01A-02 4 0.3718 0.58387 0.000 0.148 0.016 0.800 0.008 0.028
#> TCGA-06-0182-01A-01 4 0.4589 0.66684 0.000 0.008 0.144 0.752 0.040 0.056
#> TCGA-06-0185-01A-01 4 0.5515 0.60841 0.000 0.008 0.224 0.648 0.044 0.076
#> TCGA-06-0195-01B-01 4 0.7661 0.39321 0.032 0.008 0.136 0.484 0.184 0.156
#> TCGA-06-0208-01B-01 4 0.4167 0.67508 0.000 0.008 0.140 0.780 0.032 0.040
#> TCGA-06-0214-01A-02 3 0.4646 0.50504 0.000 0.128 0.728 0.128 0.012 0.004
#> TCGA-06-0219-01A-01 4 0.0951 0.63320 0.000 0.004 0.000 0.968 0.008 0.020
#> TCGA-06-0221-01A-01 4 0.0951 0.63320 0.000 0.004 0.000 0.968 0.008 0.020
#> TCGA-06-0237-01A-02 4 0.3078 0.69176 0.000 0.012 0.112 0.844 0.032 0.000
#> TCGA-06-0240-01A-02 4 0.0951 0.63411 0.000 0.004 0.000 0.968 0.008 0.020
#> TCGA-08-0349-01A-01 3 0.6711 0.35934 0.000 0.076 0.576 0.132 0.184 0.032
#> TCGA-08-0380-01A-01 4 0.4452 0.53015 0.000 0.196 0.024 0.736 0.012 0.032
#> TCGA-08-0386-01A-01 3 0.6376 -0.07150 0.204 0.000 0.488 0.004 0.024 0.280
#> TCGA-08-0520-01A-01 5 0.6244 0.30443 0.000 0.060 0.104 0.340 0.496 0.000
#> TCGA-02-0007-01A-01 6 0.6269 0.14742 0.256 0.000 0.368 0.000 0.008 0.368
#> TCGA-02-0009-01A-01 3 0.6012 -0.22298 0.244 0.000 0.408 0.000 0.000 0.348
#> TCGA-02-0016-01A-01 6 0.7412 0.19551 0.128 0.000 0.344 0.004 0.180 0.344
#> TCGA-02-0021-01A-01 3 0.5948 0.00435 0.148 0.000 0.512 0.004 0.012 0.324
#> TCGA-02-0023-01B-01 5 0.6770 0.30764 0.000 0.136 0.092 0.316 0.456 0.000
#> TCGA-02-0027-01A-01 3 0.6794 0.04888 0.040 0.004 0.496 0.012 0.256 0.192
#> TCGA-02-0038-01A-01 3 0.3974 0.56881 0.000 0.064 0.808 0.092 0.020 0.016
#> TCGA-02-0043-01A-01 3 0.6034 -0.23130 0.252 0.000 0.400 0.000 0.000 0.348
#> TCGA-02-0070-01A-01 3 0.4337 0.47468 0.000 0.016 0.748 0.004 0.060 0.172
#> TCGA-02-0102-01A-01 3 0.6027 -0.23180 0.248 0.000 0.400 0.000 0.000 0.352
#> TCGA-02-0260-01A-03 5 0.6752 0.09586 0.104 0.000 0.112 0.000 0.436 0.348
#> TCGA-02-0269-01B-01 5 0.6752 0.09586 0.104 0.000 0.112 0.000 0.436 0.348
#> TCGA-02-0285-01A-01 3 0.5079 0.47705 0.004 0.004 0.724 0.076 0.060 0.132
#> TCGA-02-0289-01A-01 5 0.6725 0.09636 0.100 0.000 0.112 0.000 0.436 0.352
#> TCGA-02-0290-01A-01 5 0.6098 0.33641 0.000 0.068 0.084 0.320 0.528 0.000
#> TCGA-02-0317-01A-01 5 0.5300 0.23572 0.000 0.000 0.092 0.008 0.560 0.340
#> TCGA-02-0333-01A-02 5 0.6725 0.09636 0.100 0.000 0.112 0.000 0.436 0.352
#> TCGA-02-0422-01A-01 3 0.4719 0.49402 0.004 0.004 0.756 0.064 0.060 0.112
#> TCGA-02-0430-01A-01 3 0.5320 0.45595 0.008 0.004 0.700 0.076 0.052 0.160
#> TCGA-06-0125-01A-01 3 0.6012 -0.22298 0.244 0.000 0.408 0.000 0.000 0.348
#> TCGA-06-0126-01A-01 3 0.6012 -0.22298 0.244 0.000 0.408 0.000 0.000 0.348
#> TCGA-06-0137-01A-03 3 0.5272 0.14760 0.072 0.000 0.588 0.000 0.020 0.320
#> TCGA-06-0145-01A-04 3 0.2808 0.54970 0.024 0.032 0.888 0.000 0.020 0.036
#> TCGA-06-0148-01A-01 3 0.5008 0.19183 0.024 0.004 0.596 0.000 0.032 0.344
#> TCGA-06-0187-01A-01 3 0.3171 0.57755 0.000 0.040 0.868 0.044 0.024 0.024
#> TCGA-06-0211-01B-01 4 0.6845 0.24324 0.000 0.000 0.312 0.396 0.052 0.240
#> TCGA-06-0402-01A-01 3 0.5948 0.00435 0.148 0.000 0.512 0.004 0.012 0.324
#> TCGA-08-0246-01A-01 3 0.6165 0.40657 0.000 0.132 0.612 0.156 0.096 0.004
#> TCGA-08-0354-01A-01 5 0.6534 0.24375 0.000 0.124 0.056 0.372 0.444 0.004
#> TCGA-08-0355-01A-01 5 0.6770 0.30764 0.000 0.136 0.092 0.316 0.456 0.000
#> TCGA-08-0357-01A-01 3 0.5741 0.51851 0.020 0.040 0.712 0.052 0.100 0.076
#> TCGA-08-0358-01A-01 5 0.3657 0.42185 0.000 0.004 0.024 0.136 0.808 0.028
#> TCGA-08-0375-01A-01 6 0.7568 0.24464 0.248 0.000 0.280 0.000 0.156 0.316
#> TCGA-08-0511-01A-01 3 0.3866 0.55864 0.000 0.028 0.828 0.044 0.056 0.044
#> TCGA-08-0514-01A-01 3 0.3398 0.57360 0.000 0.032 0.856 0.048 0.028 0.036
#> TCGA-08-0518-01A-01 3 0.5283 0.11839 0.080 0.000 0.576 0.004 0.008 0.332
#> TCGA-08-0529-01A-02 3 0.5079 0.47705 0.004 0.004 0.724 0.076 0.060 0.132
#> TCGA-08-0531-01A-01 3 0.4723 0.49537 0.004 0.004 0.752 0.076 0.044 0.120
#> TCGA-02-0057-01A-01 3 0.4354 0.33279 0.000 0.268 0.684 0.040 0.008 0.000
#> TCGA-02-0004-01A-01 2 0.1333 0.63003 0.000 0.944 0.000 0.048 0.000 0.008
#> TCGA-02-0006-01B-01 3 0.4354 0.33279 0.000 0.268 0.684 0.040 0.008 0.000
#> TCGA-02-0025-01A-01 2 0.4171 0.51450 0.000 0.776 0.000 0.132 0.048 0.044
#> TCGA-02-0033-01A-01 2 0.0458 0.64714 0.000 0.984 0.016 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.4493 0.39999 0.000 0.540 0.436 0.004 0.016 0.004
#> TCGA-02-0039-01A-01 2 0.5912 0.37728 0.000 0.476 0.396 0.092 0.036 0.000
#> TCGA-02-0051-01A-01 2 0.4644 0.33050 0.000 0.648 0.000 0.296 0.012 0.044
#> TCGA-02-0054-01A-01 3 0.4177 0.40680 0.000 0.216 0.736 0.028 0.008 0.012
#> TCGA-02-0055-01A-01 2 0.3108 0.56074 0.000 0.828 0.000 0.128 0.000 0.044
#> TCGA-02-0059-01A-01 2 0.3042 0.57730 0.000 0.836 0.004 0.128 0.000 0.032
#> TCGA-02-0064-01A-01 3 0.4419 0.10170 0.000 0.348 0.620 0.000 0.024 0.008
#> TCGA-02-0075-01A-01 3 0.4419 0.10170 0.000 0.348 0.620 0.000 0.024 0.008
#> TCGA-02-0079-01A-03 2 0.5755 0.22054 0.000 0.564 0.000 0.308 0.084 0.044
#> TCGA-02-0085-01A-01 3 0.4572 -0.03621 0.000 0.400 0.568 0.020 0.012 0.000
#> TCGA-02-0086-01A-01 2 0.5632 0.38044 0.000 0.588 0.116 0.276 0.008 0.012
#> TCGA-02-0099-01A-01 3 0.3906 0.48921 0.000 0.168 0.780 0.024 0.020 0.008
#> TCGA-02-0106-01A-01 2 0.4161 0.48195 0.000 0.608 0.376 0.000 0.012 0.004
#> TCGA-02-0107-01A-01 2 0.1434 0.62714 0.000 0.940 0.000 0.048 0.000 0.012
#> TCGA-02-0111-01A-01 2 0.3042 0.57730 0.000 0.836 0.004 0.128 0.000 0.032
#> TCGA-02-0326-01A-01 5 0.3290 0.42383 0.000 0.000 0.044 0.132 0.820 0.004
#> TCGA-02-0337-01A-01 2 0.4505 0.38246 0.000 0.528 0.448 0.004 0.016 0.004
#> TCGA-06-0122-01A-01 3 0.3198 0.53019 0.000 0.100 0.844 0.000 0.024 0.032
#> TCGA-06-0124-01A-01 3 0.4365 0.14120 0.000 0.332 0.636 0.000 0.024 0.008
#> TCGA-06-0130-01A-01 2 0.0458 0.64714 0.000 0.984 0.016 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.1434 0.62714 0.000 0.940 0.000 0.048 0.000 0.012
#> TCGA-06-0143-01A-01 3 0.2767 0.55210 0.000 0.044 0.880 0.000 0.028 0.048
#> TCGA-06-0147-01A-01 2 0.0458 0.64714 0.000 0.984 0.016 0.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.7098 0.28103 0.000 0.396 0.324 0.200 0.076 0.004
#> TCGA-06-0152-01A-02 5 0.6018 0.30660 0.000 0.092 0.048 0.356 0.504 0.000
#> TCGA-06-0154-01A-02 2 0.4400 0.36757 0.000 0.524 0.456 0.000 0.012 0.008
#> TCGA-06-0164-01A-01 2 0.2757 0.63531 0.000 0.848 0.136 0.004 0.008 0.004
#> TCGA-06-0175-01A-01 3 0.4376 -0.02059 0.000 0.384 0.592 0.000 0.012 0.012
#> TCGA-06-0176-01A-03 2 0.4375 0.40691 0.000 0.548 0.432 0.000 0.012 0.008
#> TCGA-06-0184-01A-01 2 0.5133 0.41972 0.000 0.640 0.072 0.268 0.008 0.012
#> TCGA-06-0189-01A-05 2 0.3042 0.57730 0.000 0.836 0.004 0.128 0.000 0.032
#> TCGA-06-0190-01A-01 2 0.4400 0.36757 0.000 0.524 0.456 0.000 0.012 0.008
#> TCGA-06-0194-01A-01 2 0.3733 0.64853 0.000 0.808 0.124 0.044 0.004 0.020
#> TCGA-06-0197-01A-02 2 0.3042 0.57730 0.000 0.836 0.004 0.128 0.000 0.032
#> TCGA-06-0210-01A-01 2 0.4400 0.36757 0.000 0.524 0.456 0.000 0.012 0.008
#> TCGA-06-0397-01A-01 3 0.4412 -0.28790 0.000 0.480 0.500 0.000 0.012 0.008
#> TCGA-06-0409-01A-02 2 0.3910 0.51032 0.000 0.660 0.328 0.000 0.008 0.004
#> TCGA-06-0412-01A-01 2 0.4400 0.36757 0.000 0.524 0.456 0.000 0.012 0.008
#> TCGA-06-0644-01A-02 2 0.1333 0.63003 0.000 0.944 0.000 0.048 0.000 0.008
#> TCGA-06-0645-01A-01 2 0.4087 0.52862 0.000 0.668 0.312 0.004 0.008 0.008
#> TCGA-08-0346-01A-01 2 0.4212 0.45170 0.000 0.592 0.392 0.000 0.008 0.008
#> TCGA-08-0352-01A-01 3 0.4954 0.52607 0.000 0.084 0.752 0.084 0.036 0.044
#> TCGA-08-0360-01A-01 2 0.4203 0.45671 0.000 0.596 0.388 0.000 0.008 0.008
#> TCGA-08-0390-01A-01 2 0.3916 0.52756 0.000 0.768 0.008 0.184 0.008 0.032
#> TCGA-08-0392-01A-01 2 0.4644 0.33050 0.000 0.648 0.000 0.296 0.012 0.044
#> TCGA-08-0509-01A-01 2 0.3910 0.51032 0.000 0.660 0.328 0.000 0.008 0.004
#> TCGA-08-0510-01A-01 3 0.4419 0.10170 0.000 0.348 0.620 0.000 0.024 0.008
#> TCGA-08-0512-01A-01 2 0.2994 0.60269 0.000 0.788 0.208 0.000 0.004 0.000
#> TCGA-08-0522-01A-01 2 0.0632 0.64879 0.000 0.976 0.024 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.4375 0.40691 0.000 0.548 0.432 0.000 0.012 0.008
#> TCGA-12-0620-01A-01 5 0.6665 0.25703 0.000 0.156 0.052 0.348 0.440 0.004
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> ATC:hclust 153 1.32e-15 2
#> ATC:hclust 94 9.77e-25 3
#> ATC:hclust 74 1.09e-22 4
#> ATC:hclust 92 2.49e-41 5
#> ATC:hclust 85 1.28e-31 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "kmeans"]
# you can also extract it by
# res = res_list["ATC:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.905 0.924 0.970 0.4961 0.502 0.502
#> 3 3 0.500 0.641 0.803 0.3165 0.706 0.478
#> 4 4 0.842 0.887 0.934 0.1305 0.807 0.508
#> 5 5 0.708 0.626 0.809 0.0678 0.878 0.592
#> 6 6 0.684 0.540 0.705 0.0417 0.899 0.580
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0047-01A-01 2 0.767 0.705 0.224 0.776
#> TCGA-02-0048-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0084-01A-03 2 0.000 0.971 0.000 1.000
#> TCGA-02-0087-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0104-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.788 0.684 0.764 0.236
#> TCGA-02-0325-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.000 0.962 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0446-01A-01 2 0.900 0.534 0.316 0.684
#> TCGA-06-0128-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0166-01A-01 1 0.932 0.477 0.652 0.348
#> TCGA-06-0174-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0238-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.000 0.962 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.814 0.658 0.252 0.748
#> TCGA-06-0648-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.913 0.520 0.672 0.328
#> TCGA-08-0348-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0353-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0115-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0138-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0171-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0173-01A-01 2 0.895 0.543 0.312 0.688
#> TCGA-06-0179-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0185-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0221-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0237-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0240-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-08-0349-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0520-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0007-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0009-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0016-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0021-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0023-01B-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0038-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0043-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0070-01A-01 1 0.876 0.582 0.704 0.296
#> TCGA-02-0102-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0260-01A-03 1 0.000 0.962 1.000 0.000
#> TCGA-02-0269-01B-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0285-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0289-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0290-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0317-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-02-0333-01A-02 1 0.000 0.962 1.000 0.000
#> TCGA-02-0422-01A-01 2 0.615 0.808 0.152 0.848
#> TCGA-02-0430-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0125-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0126-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0137-01A-03 1 0.000 0.962 1.000 0.000
#> TCGA-06-0145-01A-04 2 0.973 0.314 0.404 0.596
#> TCGA-06-0148-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0187-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0211-01B-01 1 0.000 0.962 1.000 0.000
#> TCGA-06-0402-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0246-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0357-01A-01 1 0.921 0.504 0.664 0.336
#> TCGA-08-0358-01A-01 2 0.995 0.109 0.460 0.540
#> TCGA-08-0375-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0511-01A-01 1 0.943 0.450 0.640 0.360
#> TCGA-08-0514-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0518-01A-01 1 0.000 0.962 1.000 0.000
#> TCGA-08-0529-01A-02 1 0.963 0.379 0.612 0.388
#> TCGA-08-0531-01A-01 1 0.992 0.201 0.552 0.448
#> TCGA-02-0057-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.000 0.971 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-02-0337-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.730 0.735 0.204 0.796
#> TCGA-06-0124-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.730 0.735 0.204 0.796
#> TCGA-06-0147-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.000 0.971 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.000 0.971 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.000 0.971 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.000 0.971 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.000 0.971 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.000 0.971 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 3 0.8141 0.6283 0.116 0.260 0.624
#> TCGA-02-0048-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.6267 0.1258 0.548 0.000 0.452
#> TCGA-02-0069-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.1031 0.8406 0.976 0.000 0.024
#> TCGA-02-0084-01A-03 3 0.5465 0.5956 0.000 0.288 0.712
#> TCGA-02-0087-01A-01 3 0.6140 0.2269 0.404 0.000 0.596
#> TCGA-02-0104-01A-01 1 0.4235 0.6671 0.824 0.000 0.176
#> TCGA-02-0114-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.3192 0.6065 0.112 0.000 0.888
#> TCGA-02-0325-01A-01 1 0.2066 0.8286 0.940 0.000 0.060
#> TCGA-02-0338-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0237 0.8468 0.996 0.000 0.004
#> TCGA-02-0432-01A-02 1 0.0892 0.8412 0.980 0.000 0.020
#> TCGA-02-0439-01A-01 3 0.5835 0.3702 0.340 0.000 0.660
#> TCGA-02-0440-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 3 0.8349 0.6228 0.128 0.264 0.608
#> TCGA-06-0128-01A-01 3 0.6267 0.2335 0.452 0.000 0.548
#> TCGA-06-0129-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0424 0.8456 0.992 0.000 0.008
#> TCGA-06-0156-01A-01 3 0.6062 0.3181 0.384 0.000 0.616
#> TCGA-06-0166-01A-01 3 0.8266 0.6334 0.136 0.240 0.624
#> TCGA-06-0174-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0424 0.8456 0.992 0.000 0.008
#> TCGA-06-0238-01A-02 3 0.3038 0.6248 0.000 0.104 0.896
#> TCGA-06-0241-01A-02 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-06-0410-01A-01 3 0.5706 0.4532 0.320 0.000 0.680
#> TCGA-06-0413-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.8021 0.6343 0.124 0.232 0.644
#> TCGA-06-0648-01A-01 1 0.1529 0.8312 0.960 0.000 0.040
#> TCGA-08-0245-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0237 0.8468 0.996 0.000 0.004
#> TCGA-08-0347-01A-01 3 0.8001 0.6278 0.136 0.212 0.652
#> TCGA-08-0348-01A-01 1 0.6252 0.1242 0.556 0.000 0.444
#> TCGA-08-0350-01A-01 1 0.6225 0.1776 0.568 0.000 0.432
#> TCGA-08-0353-01A-01 1 0.3116 0.7917 0.892 0.000 0.108
#> TCGA-08-0359-01A-01 3 0.5882 0.3626 0.348 0.000 0.652
#> TCGA-08-0385-01A-01 1 0.1529 0.8312 0.960 0.000 0.040
#> TCGA-08-0517-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.8484 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 3 0.3482 0.5983 0.128 0.000 0.872
#> TCGA-12-0618-01A-01 1 0.0237 0.8468 0.996 0.000 0.004
#> TCGA-02-0089-01A-01 2 0.2625 0.8152 0.000 0.916 0.084
#> TCGA-02-0113-01A-01 3 0.5678 0.5698 0.000 0.316 0.684
#> TCGA-02-0115-01A-01 3 0.6307 0.3293 0.000 0.488 0.512
#> TCGA-02-0451-01A-01 2 0.2878 0.7918 0.000 0.904 0.096
#> TCGA-06-0132-01A-02 2 0.5905 0.5386 0.000 0.648 0.352
#> TCGA-06-0133-01A-02 3 0.4291 0.5686 0.000 0.180 0.820
#> TCGA-06-0138-01A-02 3 0.4178 0.5786 0.000 0.172 0.828
#> TCGA-06-0160-01A-01 3 0.5016 0.5206 0.240 0.000 0.760
#> TCGA-06-0162-01A-01 2 0.6302 0.2995 0.000 0.520 0.480
#> TCGA-06-0167-01A-01 3 0.4887 0.5329 0.228 0.000 0.772
#> TCGA-06-0171-01A-02 3 0.3619 0.6109 0.000 0.136 0.864
#> TCGA-06-0173-01A-01 3 0.8278 0.6336 0.132 0.248 0.620
#> TCGA-06-0179-01A-02 2 0.6291 0.3252 0.000 0.532 0.468
#> TCGA-06-0182-01A-01 3 0.4178 0.5786 0.000 0.172 0.828
#> TCGA-06-0185-01A-01 3 0.3038 0.6312 0.000 0.104 0.896
#> TCGA-06-0195-01B-01 3 0.4654 0.5576 0.208 0.000 0.792
#> TCGA-06-0208-01B-01 3 0.4178 0.5786 0.000 0.172 0.828
#> TCGA-06-0214-01A-02 3 0.6274 0.4251 0.000 0.456 0.544
#> TCGA-06-0219-01A-01 3 0.4399 0.5578 0.000 0.188 0.812
#> TCGA-06-0221-01A-01 3 0.4121 0.5804 0.000 0.168 0.832
#> TCGA-06-0237-01A-02 3 0.3340 0.6203 0.000 0.120 0.880
#> TCGA-06-0240-01A-02 3 0.4121 0.5804 0.000 0.168 0.832
#> TCGA-08-0349-01A-01 3 0.3686 0.6349 0.000 0.140 0.860
#> TCGA-08-0380-01A-01 2 0.6126 0.4584 0.000 0.600 0.400
#> TCGA-08-0386-01A-01 1 0.6299 0.1169 0.524 0.000 0.476
#> TCGA-08-0520-01A-01 3 0.3619 0.6109 0.000 0.136 0.864
#> TCGA-02-0007-01A-01 1 0.5926 0.4347 0.644 0.000 0.356
#> TCGA-02-0009-01A-01 1 0.3267 0.7859 0.884 0.000 0.116
#> TCGA-02-0016-01A-01 3 0.6305 -0.0396 0.484 0.000 0.516
#> TCGA-02-0021-01A-01 1 0.6299 0.1169 0.524 0.000 0.476
#> TCGA-02-0023-01B-01 3 0.2537 0.6356 0.000 0.080 0.920
#> TCGA-02-0027-01A-01 1 0.6302 0.1158 0.520 0.000 0.480
#> TCGA-02-0038-01A-01 3 0.6079 0.4970 0.000 0.388 0.612
#> TCGA-02-0043-01A-01 1 0.2959 0.7964 0.900 0.000 0.100
#> TCGA-02-0070-01A-01 3 0.8113 0.6204 0.144 0.212 0.644
#> TCGA-02-0102-01A-01 1 0.3340 0.7831 0.880 0.000 0.120
#> TCGA-02-0260-01A-03 1 0.1643 0.8355 0.956 0.000 0.044
#> TCGA-02-0269-01B-01 1 0.4178 0.7521 0.828 0.000 0.172
#> TCGA-02-0285-01A-01 3 0.5859 0.5464 0.000 0.344 0.656
#> TCGA-02-0289-01A-01 3 0.6295 -0.0136 0.472 0.000 0.528
#> TCGA-02-0290-01A-01 3 0.4002 0.5886 0.000 0.160 0.840
#> TCGA-02-0317-01A-01 3 0.2796 0.6140 0.092 0.000 0.908
#> TCGA-02-0333-01A-02 1 0.6168 0.3443 0.588 0.000 0.412
#> TCGA-02-0422-01A-01 3 0.8043 0.6327 0.128 0.228 0.644
#> TCGA-02-0430-01A-01 1 0.6308 0.0600 0.508 0.000 0.492
#> TCGA-06-0125-01A-01 1 0.3038 0.7942 0.896 0.000 0.104
#> TCGA-06-0126-01A-01 1 0.3340 0.7859 0.880 0.000 0.120
#> TCGA-06-0137-01A-03 3 0.6309 -0.0862 0.500 0.000 0.500
#> TCGA-06-0145-01A-04 3 0.8278 0.6250 0.132 0.248 0.620
#> TCGA-06-0148-01A-01 3 0.7809 0.2197 0.396 0.056 0.548
#> TCGA-06-0187-01A-01 3 0.6095 0.4901 0.000 0.392 0.608
#> TCGA-06-0211-01B-01 3 0.5948 0.3536 0.360 0.000 0.640
#> TCGA-06-0402-01A-01 1 0.6299 0.1169 0.524 0.000 0.476
#> TCGA-08-0246-01A-01 3 0.6305 0.3734 0.000 0.484 0.516
#> TCGA-08-0354-01A-01 3 0.6309 -0.2659 0.000 0.496 0.504
#> TCGA-08-0355-01A-01 3 0.2796 0.6319 0.000 0.092 0.908
#> TCGA-08-0357-01A-01 3 0.8042 0.6293 0.136 0.216 0.648
#> TCGA-08-0358-01A-01 3 0.2625 0.6340 0.000 0.084 0.916
#> TCGA-08-0375-01A-01 1 0.3412 0.7830 0.876 0.000 0.124
#> TCGA-08-0511-01A-01 3 0.8321 0.6218 0.140 0.240 0.620
#> TCGA-08-0514-01A-01 3 0.6045 0.5049 0.000 0.380 0.620
#> TCGA-08-0518-01A-01 1 0.6308 0.0742 0.508 0.000 0.492
#> TCGA-08-0529-01A-02 3 0.8081 0.6290 0.136 0.220 0.644
#> TCGA-08-0531-01A-01 3 0.8042 0.6293 0.136 0.216 0.648
#> TCGA-02-0057-01A-01 3 0.6307 0.3006 0.000 0.488 0.512
#> TCGA-02-0004-01A-01 2 0.1031 0.8603 0.000 0.976 0.024
#> TCGA-02-0006-01B-01 2 0.1031 0.8490 0.000 0.976 0.024
#> TCGA-02-0025-01A-01 2 0.3752 0.7852 0.000 0.856 0.144
#> TCGA-02-0033-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-02-0039-01A-01 2 0.0892 0.8614 0.000 0.980 0.020
#> TCGA-02-0051-01A-01 2 0.3816 0.7819 0.000 0.852 0.148
#> TCGA-02-0054-01A-01 2 0.3412 0.7508 0.000 0.876 0.124
#> TCGA-02-0055-01A-01 2 0.2537 0.8333 0.000 0.920 0.080
#> TCGA-02-0059-01A-01 2 0.3879 0.7782 0.000 0.848 0.152
#> TCGA-02-0064-01A-01 2 0.2261 0.8067 0.000 0.932 0.068
#> TCGA-02-0075-01A-01 2 0.3038 0.7651 0.000 0.896 0.104
#> TCGA-02-0079-01A-03 2 0.5650 0.5923 0.000 0.688 0.312
#> TCGA-02-0085-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-02-0086-01A-01 2 0.0747 0.8622 0.000 0.984 0.016
#> TCGA-02-0099-01A-01 2 0.6302 -0.2529 0.000 0.520 0.480
#> TCGA-02-0106-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-02-0107-01A-01 2 0.1031 0.8603 0.000 0.976 0.024
#> TCGA-02-0111-01A-01 2 0.3267 0.8080 0.000 0.884 0.116
#> TCGA-02-0326-01A-01 3 0.2711 0.6325 0.000 0.088 0.912
#> TCGA-02-0337-01A-01 2 0.0237 0.8635 0.000 0.996 0.004
#> TCGA-06-0122-01A-01 3 0.6521 0.2874 0.004 0.492 0.504
#> TCGA-06-0124-01A-01 2 0.2796 0.7799 0.000 0.908 0.092
#> TCGA-06-0130-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.2537 0.8333 0.000 0.920 0.080
#> TCGA-06-0143-01A-01 3 0.6520 0.2980 0.004 0.488 0.508
#> TCGA-06-0147-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-06-0152-01A-02 3 0.3879 0.5906 0.000 0.152 0.848
#> TCGA-06-0154-01A-02 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 2 0.6305 -0.2644 0.000 0.516 0.484
#> TCGA-06-0176-01A-03 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.2537 0.8333 0.000 0.920 0.080
#> TCGA-06-0189-01A-05 2 0.3879 0.7782 0.000 0.848 0.152
#> TCGA-06-0190-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.1031 0.8603 0.000 0.976 0.024
#> TCGA-06-0197-01A-02 2 0.2625 0.8308 0.000 0.916 0.084
#> TCGA-06-0210-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-06-0397-01A-01 2 0.1289 0.8425 0.000 0.968 0.032
#> TCGA-06-0409-01A-02 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-06-0412-01A-01 2 0.1163 0.8458 0.000 0.972 0.028
#> TCGA-06-0644-01A-02 2 0.1031 0.8603 0.000 0.976 0.024
#> TCGA-06-0645-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-08-0352-01A-01 2 0.5098 0.5247 0.000 0.752 0.248
#> TCGA-08-0360-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.3879 0.7782 0.000 0.848 0.152
#> TCGA-08-0392-01A-01 2 0.5835 0.5472 0.000 0.660 0.340
#> TCGA-08-0509-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 2 0.2711 0.7838 0.000 0.912 0.088
#> TCGA-08-0512-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8650 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 2 0.0747 0.8549 0.000 0.984 0.016
#> TCGA-12-0620-01A-01 2 0.3941 0.7750 0.000 0.844 0.156
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 3 0.2629 0.8974 0.004 0.060 0.912 0.024
#> TCGA-02-0048-01A-01 1 0.0188 0.9516 0.996 0.000 0.004 0.000
#> TCGA-02-0060-01A-01 3 0.1411 0.8885 0.020 0.000 0.960 0.020
#> TCGA-02-0069-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.2775 0.8828 0.896 0.000 0.084 0.020
#> TCGA-02-0084-01A-03 3 0.0895 0.8952 0.000 0.004 0.976 0.020
#> TCGA-02-0087-01A-01 3 0.1174 0.8914 0.012 0.000 0.968 0.020
#> TCGA-02-0104-01A-01 1 0.2530 0.8555 0.888 0.000 0.000 0.112
#> TCGA-02-0114-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.0921 0.8911 0.000 0.000 0.972 0.028
#> TCGA-02-0325-01A-01 1 0.5607 0.0646 0.496 0.000 0.484 0.020
#> TCGA-02-0338-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.2775 0.8828 0.896 0.000 0.084 0.020
#> TCGA-02-0439-01A-01 3 0.0707 0.8945 0.000 0.000 0.980 0.020
#> TCGA-02-0440-01A-01 1 0.0188 0.9516 0.996 0.000 0.004 0.000
#> TCGA-02-0446-01A-01 3 0.2774 0.8981 0.008 0.060 0.908 0.024
#> TCGA-06-0128-01A-01 3 0.6037 0.6900 0.160 0.000 0.688 0.152
#> TCGA-06-0129-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.1557 0.9175 0.944 0.000 0.056 0.000
#> TCGA-06-0156-01A-01 3 0.2443 0.8982 0.060 0.000 0.916 0.024
#> TCGA-06-0166-01A-01 3 0.2613 0.9000 0.008 0.052 0.916 0.024
#> TCGA-06-0174-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.1978 0.9082 0.928 0.000 0.068 0.004
#> TCGA-06-0238-01A-02 4 0.0921 0.9078 0.000 0.000 0.028 0.972
#> TCGA-06-0241-01A-02 1 0.0188 0.9516 0.996 0.000 0.004 0.000
#> TCGA-06-0410-01A-01 4 0.3991 0.8137 0.120 0.000 0.048 0.832
#> TCGA-06-0413-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0188 0.9516 0.996 0.000 0.004 0.000
#> TCGA-06-0646-01A-01 3 0.2467 0.9005 0.004 0.052 0.920 0.024
#> TCGA-06-0648-01A-01 1 0.2843 0.8812 0.892 0.000 0.088 0.020
#> TCGA-08-0245-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 3 0.0672 0.9028 0.000 0.008 0.984 0.008
#> TCGA-08-0348-01A-01 3 0.1661 0.8998 0.052 0.000 0.944 0.004
#> TCGA-08-0350-01A-01 3 0.3853 0.7653 0.160 0.000 0.820 0.020
#> TCGA-08-0353-01A-01 3 0.3610 0.8017 0.200 0.000 0.800 0.000
#> TCGA-08-0359-01A-01 3 0.0592 0.8956 0.000 0.000 0.984 0.016
#> TCGA-08-0385-01A-01 1 0.2775 0.8828 0.896 0.000 0.084 0.020
#> TCGA-08-0517-01A-01 1 0.0188 0.9516 0.996 0.000 0.004 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 4 0.1302 0.9030 0.000 0.000 0.044 0.956
#> TCGA-12-0618-01A-01 1 0.0000 0.9535 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.1936 0.9268 0.000 0.940 0.028 0.032
#> TCGA-02-0113-01A-01 4 0.4289 0.7558 0.000 0.032 0.172 0.796
#> TCGA-02-0115-01A-01 4 0.5874 0.6836 0.000 0.176 0.124 0.700
#> TCGA-02-0451-01A-01 2 0.3080 0.8628 0.000 0.880 0.096 0.024
#> TCGA-06-0132-01A-02 4 0.4967 0.1823 0.000 0.452 0.000 0.548
#> TCGA-06-0133-01A-02 4 0.0779 0.9167 0.000 0.016 0.004 0.980
#> TCGA-06-0138-01A-02 4 0.0779 0.9167 0.000 0.016 0.004 0.980
#> TCGA-06-0160-01A-01 4 0.2408 0.8783 0.000 0.000 0.104 0.896
#> TCGA-06-0162-01A-01 4 0.0707 0.9149 0.000 0.020 0.000 0.980
#> TCGA-06-0167-01A-01 4 0.2408 0.8783 0.000 0.000 0.104 0.896
#> TCGA-06-0171-01A-02 4 0.0804 0.9168 0.000 0.012 0.008 0.980
#> TCGA-06-0173-01A-01 3 0.2613 0.9000 0.008 0.052 0.916 0.024
#> TCGA-06-0179-01A-02 4 0.0707 0.9149 0.000 0.020 0.000 0.980
#> TCGA-06-0182-01A-01 4 0.0804 0.9168 0.000 0.012 0.008 0.980
#> TCGA-06-0185-01A-01 4 0.0937 0.9168 0.000 0.012 0.012 0.976
#> TCGA-06-0195-01B-01 4 0.1807 0.9002 0.008 0.000 0.052 0.940
#> TCGA-06-0208-01B-01 4 0.0804 0.9168 0.000 0.012 0.008 0.980
#> TCGA-06-0214-01A-02 3 0.3143 0.8724 0.000 0.100 0.876 0.024
#> TCGA-06-0219-01A-01 4 0.0779 0.9167 0.000 0.016 0.004 0.980
#> TCGA-06-0221-01A-01 4 0.0779 0.9167 0.000 0.016 0.004 0.980
#> TCGA-06-0237-01A-02 4 0.0937 0.9168 0.000 0.012 0.012 0.976
#> TCGA-06-0240-01A-02 4 0.0779 0.9167 0.000 0.016 0.004 0.980
#> TCGA-08-0349-01A-01 4 0.1975 0.9032 0.000 0.016 0.048 0.936
#> TCGA-08-0380-01A-01 4 0.4697 0.4496 0.000 0.356 0.000 0.644
#> TCGA-08-0386-01A-01 3 0.2081 0.8936 0.084 0.000 0.916 0.000
#> TCGA-08-0520-01A-01 4 0.0937 0.9168 0.000 0.012 0.012 0.976
#> TCGA-02-0007-01A-01 3 0.2149 0.8918 0.088 0.000 0.912 0.000
#> TCGA-02-0009-01A-01 3 0.4103 0.7296 0.256 0.000 0.744 0.000
#> TCGA-02-0016-01A-01 3 0.0336 0.8982 0.000 0.000 0.992 0.008
#> TCGA-02-0021-01A-01 3 0.2081 0.8936 0.084 0.000 0.916 0.000
#> TCGA-02-0023-01B-01 4 0.2216 0.8842 0.000 0.000 0.092 0.908
#> TCGA-02-0027-01A-01 3 0.1209 0.9041 0.032 0.000 0.964 0.004
#> TCGA-02-0038-01A-01 3 0.2521 0.8953 0.000 0.064 0.912 0.024
#> TCGA-02-0043-01A-01 3 0.4713 0.5496 0.360 0.000 0.640 0.000
#> TCGA-02-0070-01A-01 3 0.0188 0.9009 0.000 0.004 0.996 0.000
#> TCGA-02-0102-01A-01 3 0.2589 0.8764 0.116 0.000 0.884 0.000
#> TCGA-02-0260-01A-03 1 0.5038 0.6053 0.684 0.000 0.296 0.020
#> TCGA-02-0269-01B-01 3 0.4675 0.6478 0.244 0.000 0.736 0.020
#> TCGA-02-0285-01A-01 3 0.1733 0.9039 0.000 0.028 0.948 0.024
#> TCGA-02-0289-01A-01 3 0.0707 0.8945 0.000 0.000 0.980 0.020
#> TCGA-02-0290-01A-01 4 0.1406 0.9144 0.000 0.016 0.024 0.960
#> TCGA-02-0317-01A-01 3 0.1867 0.8639 0.000 0.000 0.928 0.072
#> TCGA-02-0333-01A-02 3 0.0707 0.8945 0.000 0.000 0.980 0.020
#> TCGA-02-0422-01A-01 3 0.1733 0.9039 0.000 0.028 0.948 0.024
#> TCGA-02-0430-01A-01 3 0.2081 0.8936 0.084 0.000 0.916 0.000
#> TCGA-06-0125-01A-01 3 0.4697 0.5580 0.356 0.000 0.644 0.000
#> TCGA-06-0126-01A-01 3 0.4331 0.6814 0.288 0.000 0.712 0.000
#> TCGA-06-0137-01A-03 3 0.0524 0.8996 0.004 0.000 0.988 0.008
#> TCGA-06-0145-01A-04 3 0.2629 0.8974 0.004 0.060 0.912 0.024
#> TCGA-06-0148-01A-01 3 0.0336 0.8982 0.000 0.000 0.992 0.008
#> TCGA-06-0187-01A-01 3 0.2521 0.8953 0.000 0.064 0.912 0.024
#> TCGA-06-0211-01B-01 3 0.2443 0.8982 0.060 0.000 0.916 0.024
#> TCGA-06-0402-01A-01 3 0.2081 0.8936 0.084 0.000 0.916 0.000
#> TCGA-08-0246-01A-01 2 0.5161 0.5462 0.000 0.676 0.300 0.024
#> TCGA-08-0354-01A-01 4 0.0779 0.9167 0.000 0.016 0.004 0.980
#> TCGA-08-0355-01A-01 4 0.2149 0.8866 0.000 0.000 0.088 0.912
#> TCGA-08-0357-01A-01 3 0.1284 0.9031 0.000 0.012 0.964 0.024
#> TCGA-08-0358-01A-01 4 0.2216 0.8800 0.000 0.000 0.092 0.908
#> TCGA-08-0375-01A-01 3 0.4283 0.6675 0.256 0.000 0.740 0.004
#> TCGA-08-0511-01A-01 3 0.2549 0.8986 0.004 0.056 0.916 0.024
#> TCGA-08-0514-01A-01 3 0.2443 0.8969 0.000 0.060 0.916 0.024
#> TCGA-08-0518-01A-01 3 0.2124 0.9002 0.068 0.008 0.924 0.000
#> TCGA-08-0529-01A-02 3 0.1920 0.9044 0.004 0.028 0.944 0.024
#> TCGA-08-0531-01A-01 3 0.1920 0.9044 0.004 0.028 0.944 0.024
#> TCGA-02-0057-01A-01 3 0.2216 0.8857 0.000 0.092 0.908 0.000
#> TCGA-02-0004-01A-01 2 0.0336 0.9577 0.000 0.992 0.000 0.008
#> TCGA-02-0006-01B-01 2 0.1022 0.9398 0.000 0.968 0.032 0.000
#> TCGA-02-0025-01A-01 2 0.0592 0.9544 0.000 0.984 0.000 0.016
#> TCGA-02-0033-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0336 0.9577 0.000 0.992 0.000 0.008
#> TCGA-02-0051-01A-01 2 0.0921 0.9460 0.000 0.972 0.000 0.028
#> TCGA-02-0054-01A-01 2 0.2530 0.8667 0.000 0.888 0.112 0.000
#> TCGA-02-0055-01A-01 2 0.0592 0.9544 0.000 0.984 0.000 0.016
#> TCGA-02-0059-01A-01 2 0.0921 0.9460 0.000 0.972 0.000 0.028
#> TCGA-02-0064-01A-01 2 0.0336 0.9549 0.000 0.992 0.008 0.000
#> TCGA-02-0075-01A-01 2 0.2469 0.8708 0.000 0.892 0.108 0.000
#> TCGA-02-0079-01A-03 2 0.4633 0.7340 0.000 0.780 0.048 0.172
#> TCGA-02-0085-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-02-0086-01A-01 2 0.0336 0.9577 0.000 0.992 0.000 0.008
#> TCGA-02-0099-01A-01 3 0.2647 0.8633 0.000 0.120 0.880 0.000
#> TCGA-02-0106-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0336 0.9577 0.000 0.992 0.000 0.008
#> TCGA-02-0111-01A-01 2 0.0592 0.9544 0.000 0.984 0.000 0.016
#> TCGA-02-0326-01A-01 4 0.2149 0.8819 0.000 0.000 0.088 0.912
#> TCGA-02-0337-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-06-0122-01A-01 3 0.2216 0.8857 0.000 0.092 0.908 0.000
#> TCGA-06-0124-01A-01 2 0.2149 0.8913 0.000 0.912 0.088 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0592 0.9544 0.000 0.984 0.000 0.016
#> TCGA-06-0143-01A-01 3 0.2216 0.8857 0.000 0.092 0.908 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-06-0152-01A-02 4 0.1792 0.8948 0.000 0.000 0.068 0.932
#> TCGA-06-0154-01A-02 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.2647 0.8633 0.000 0.120 0.880 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.0592 0.9544 0.000 0.984 0.000 0.016
#> TCGA-06-0189-01A-05 2 0.0921 0.9460 0.000 0.972 0.000 0.028
#> TCGA-06-0190-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0336 0.9577 0.000 0.992 0.000 0.008
#> TCGA-06-0197-01A-02 2 0.0592 0.9544 0.000 0.984 0.000 0.016
#> TCGA-06-0210-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0469 0.9530 0.000 0.988 0.012 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.1118 0.9370 0.000 0.964 0.036 0.000
#> TCGA-06-0644-01A-02 2 0.0336 0.9577 0.000 0.992 0.000 0.008
#> TCGA-06-0645-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-08-0352-01A-01 2 0.3172 0.8100 0.000 0.840 0.160 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.0921 0.9460 0.000 0.972 0.000 0.028
#> TCGA-08-0392-01A-01 2 0.3801 0.7202 0.000 0.780 0.000 0.220
#> TCGA-08-0509-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-08-0510-01A-01 2 0.2408 0.8750 0.000 0.896 0.104 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9591 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0188 0.9574 0.000 0.996 0.004 0.000
#> TCGA-12-0620-01A-01 2 0.0592 0.9544 0.000 0.984 0.000 0.016
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.2286 0.842892 0.888 0.000 0.004 0.000 0.108
#> TCGA-02-0010-01A-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0510 0.886138 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0014-01A-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0324 0.887178 0.992 0.000 0.004 0.000 0.004
#> TCGA-02-0047-01A-01 3 0.2228 0.611448 0.000 0.004 0.908 0.012 0.076
#> TCGA-02-0048-01A-01 1 0.2536 0.827163 0.868 0.000 0.004 0.000 0.128
#> TCGA-02-0060-01A-01 5 0.2956 0.630072 0.004 0.000 0.140 0.008 0.848
#> TCGA-02-0069-01A-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0324 0.887178 0.992 0.000 0.004 0.000 0.004
#> TCGA-02-0080-01A-01 1 0.4304 0.123225 0.516 0.000 0.000 0.000 0.484
#> TCGA-02-0084-01A-03 5 0.4759 0.363006 0.000 0.004 0.388 0.016 0.592
#> TCGA-02-0087-01A-01 5 0.2929 0.655228 0.004 0.000 0.128 0.012 0.856
#> TCGA-02-0104-01A-01 1 0.5051 0.607230 0.680 0.000 0.004 0.248 0.068
#> TCGA-02-0114-01A-01 1 0.0162 0.888345 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0281-01A-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.2969 0.646283 0.000 0.000 0.128 0.020 0.852
#> TCGA-02-0325-01A-01 5 0.3327 0.632591 0.144 0.000 0.028 0.000 0.828
#> TCGA-02-0338-01A-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.4287 0.197098 0.540 0.000 0.000 0.000 0.460
#> TCGA-02-0439-01A-01 5 0.3596 0.576368 0.000 0.000 0.212 0.012 0.776
#> TCGA-02-0440-01A-01 1 0.2930 0.793038 0.832 0.000 0.004 0.000 0.164
#> TCGA-02-0446-01A-01 3 0.1798 0.613163 0.000 0.004 0.928 0.004 0.064
#> TCGA-06-0128-01A-01 4 0.6389 0.245282 0.004 0.000 0.216 0.540 0.240
#> TCGA-06-0129-01A-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.2891 0.733500 0.824 0.000 0.000 0.000 0.176
#> TCGA-06-0156-01A-01 3 0.3618 0.587794 0.004 0.000 0.788 0.012 0.196
#> TCGA-06-0166-01A-01 3 0.3320 0.600552 0.000 0.004 0.820 0.012 0.164
#> TCGA-06-0174-01A-01 1 0.2233 0.845674 0.892 0.000 0.004 0.000 0.104
#> TCGA-06-0177-01A-01 1 0.4310 0.461007 0.604 0.000 0.004 0.000 0.392
#> TCGA-06-0238-01A-02 4 0.0992 0.785029 0.000 0.000 0.008 0.968 0.024
#> TCGA-06-0241-01A-02 1 0.2930 0.793038 0.832 0.000 0.004 0.000 0.164
#> TCGA-06-0410-01A-01 4 0.3844 0.679735 0.008 0.000 0.040 0.808 0.144
#> TCGA-06-0413-01A-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.2930 0.793038 0.832 0.000 0.004 0.000 0.164
#> TCGA-06-0646-01A-01 3 0.2228 0.614034 0.000 0.004 0.908 0.012 0.076
#> TCGA-06-0648-01A-01 5 0.4074 0.144037 0.364 0.000 0.000 0.000 0.636
#> TCGA-08-0245-01A-01 1 0.1704 0.865086 0.928 0.000 0.004 0.000 0.068
#> TCGA-08-0344-01A-01 1 0.0510 0.886138 0.984 0.000 0.000 0.000 0.016
#> TCGA-08-0347-01A-01 3 0.4040 0.562991 0.000 0.000 0.724 0.016 0.260
#> TCGA-08-0348-01A-01 3 0.4637 0.393922 0.004 0.000 0.568 0.008 0.420
#> TCGA-08-0350-01A-01 5 0.2544 0.659474 0.028 0.000 0.064 0.008 0.900
#> TCGA-08-0353-01A-01 3 0.5911 0.335531 0.104 0.000 0.488 0.000 0.408
#> TCGA-08-0359-01A-01 5 0.3916 0.510875 0.000 0.000 0.256 0.012 0.732
#> TCGA-08-0385-01A-01 5 0.4242 -0.040800 0.428 0.000 0.000 0.000 0.572
#> TCGA-08-0517-01A-01 1 0.2719 0.811031 0.852 0.000 0.004 0.000 0.144
#> TCGA-08-0524-01A-01 1 0.0000 0.889053 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 4 0.2331 0.756979 0.000 0.000 0.020 0.900 0.080
#> TCGA-12-0618-01A-01 1 0.0609 0.885229 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0089-01A-01 3 0.4973 -0.271813 0.000 0.480 0.496 0.020 0.004
#> TCGA-02-0113-01A-01 4 0.4670 0.154122 0.000 0.008 0.440 0.548 0.004
#> TCGA-02-0115-01A-01 3 0.4886 0.343803 0.000 0.036 0.648 0.312 0.004
#> TCGA-02-0451-01A-01 3 0.4017 0.419308 0.000 0.248 0.736 0.012 0.004
#> TCGA-06-0132-01A-02 4 0.4702 0.159623 0.000 0.476 0.004 0.512 0.008
#> TCGA-06-0133-01A-02 4 0.0566 0.790668 0.000 0.012 0.004 0.984 0.000
#> TCGA-06-0138-01A-02 4 0.0162 0.791240 0.000 0.004 0.000 0.996 0.000
#> TCGA-06-0160-01A-01 4 0.5114 0.205453 0.000 0.000 0.036 0.488 0.476
#> TCGA-06-0162-01A-01 4 0.1908 0.748298 0.000 0.092 0.000 0.908 0.000
#> TCGA-06-0167-01A-01 4 0.5111 0.237048 0.000 0.000 0.036 0.500 0.464
#> TCGA-06-0171-01A-02 4 0.0451 0.790638 0.000 0.004 0.008 0.988 0.000
#> TCGA-06-0173-01A-01 3 0.2228 0.613424 0.000 0.004 0.908 0.012 0.076
#> TCGA-06-0179-01A-02 4 0.0771 0.788621 0.000 0.020 0.004 0.976 0.000
#> TCGA-06-0182-01A-01 4 0.0451 0.791282 0.000 0.008 0.004 0.988 0.000
#> TCGA-06-0185-01A-01 4 0.0579 0.788614 0.000 0.000 0.008 0.984 0.008
#> TCGA-06-0195-01B-01 4 0.2616 0.749515 0.000 0.000 0.036 0.888 0.076
#> TCGA-06-0208-01B-01 4 0.0451 0.791282 0.000 0.008 0.004 0.988 0.000
#> TCGA-06-0214-01A-02 3 0.1885 0.594886 0.000 0.020 0.936 0.012 0.032
#> TCGA-06-0219-01A-01 4 0.0404 0.790483 0.000 0.012 0.000 0.988 0.000
#> TCGA-06-0221-01A-01 4 0.0566 0.790780 0.000 0.012 0.004 0.984 0.000
#> TCGA-06-0237-01A-02 4 0.0451 0.789021 0.000 0.000 0.008 0.988 0.004
#> TCGA-06-0240-01A-02 4 0.0566 0.790780 0.000 0.012 0.004 0.984 0.000
#> TCGA-08-0349-01A-01 4 0.3667 0.684808 0.000 0.000 0.140 0.812 0.048
#> TCGA-08-0380-01A-01 4 0.4538 0.477974 0.000 0.348 0.004 0.636 0.012
#> TCGA-08-0386-01A-01 3 0.4415 0.485849 0.008 0.000 0.604 0.000 0.388
#> TCGA-08-0520-01A-01 4 0.0451 0.788584 0.000 0.000 0.004 0.988 0.008
#> TCGA-02-0007-01A-01 3 0.4505 0.472367 0.012 0.000 0.604 0.000 0.384
#> TCGA-02-0009-01A-01 3 0.5467 0.404103 0.068 0.000 0.548 0.000 0.384
#> TCGA-02-0016-01A-01 5 0.4359 0.000103 0.000 0.000 0.412 0.004 0.584
#> TCGA-02-0021-01A-01 3 0.4380 0.484734 0.008 0.000 0.616 0.000 0.376
#> TCGA-02-0023-01B-01 4 0.4448 0.218458 0.000 0.000 0.004 0.516 0.480
#> TCGA-02-0027-01A-01 3 0.4161 0.462620 0.000 0.000 0.608 0.000 0.392
#> TCGA-02-0038-01A-01 3 0.1646 0.618649 0.000 0.020 0.944 0.004 0.032
#> TCGA-02-0043-01A-01 3 0.6409 0.236301 0.180 0.000 0.468 0.000 0.352
#> TCGA-02-0070-01A-01 3 0.4101 0.516287 0.000 0.000 0.664 0.004 0.332
#> TCGA-02-0102-01A-01 3 0.4768 0.462046 0.024 0.000 0.592 0.000 0.384
#> TCGA-02-0260-01A-03 5 0.4292 0.476291 0.272 0.000 0.024 0.000 0.704
#> TCGA-02-0269-01B-01 5 0.2484 0.660421 0.028 0.000 0.068 0.004 0.900
#> TCGA-02-0285-01A-01 3 0.2351 0.614021 0.000 0.000 0.896 0.016 0.088
#> TCGA-02-0289-01A-01 5 0.2011 0.653899 0.000 0.000 0.088 0.004 0.908
#> TCGA-02-0290-01A-01 4 0.2890 0.699955 0.000 0.004 0.000 0.836 0.160
#> TCGA-02-0317-01A-01 5 0.2069 0.658105 0.000 0.000 0.076 0.012 0.912
#> TCGA-02-0333-01A-02 5 0.2112 0.655458 0.004 0.000 0.084 0.004 0.908
#> TCGA-02-0422-01A-01 3 0.3779 0.568005 0.000 0.000 0.752 0.012 0.236
#> TCGA-02-0430-01A-01 3 0.4380 0.484734 0.008 0.000 0.616 0.000 0.376
#> TCGA-06-0125-01A-01 3 0.6281 0.275734 0.160 0.000 0.488 0.000 0.352
#> TCGA-06-0126-01A-01 3 0.5946 0.326971 0.112 0.000 0.508 0.000 0.380
#> TCGA-06-0137-01A-03 3 0.4415 0.379876 0.000 0.000 0.552 0.004 0.444
#> TCGA-06-0145-01A-04 3 0.2170 0.620573 0.000 0.004 0.904 0.004 0.088
#> TCGA-06-0148-01A-01 5 0.4196 0.181840 0.000 0.000 0.356 0.004 0.640
#> TCGA-06-0187-01A-01 3 0.1682 0.621020 0.000 0.012 0.940 0.004 0.044
#> TCGA-06-0211-01B-01 3 0.4497 0.499205 0.000 0.000 0.632 0.016 0.352
#> TCGA-06-0402-01A-01 3 0.4367 0.489051 0.008 0.000 0.620 0.000 0.372
#> TCGA-08-0246-01A-01 3 0.3317 0.498786 0.000 0.188 0.804 0.004 0.004
#> TCGA-08-0354-01A-01 4 0.1018 0.786643 0.000 0.016 0.000 0.968 0.016
#> TCGA-08-0355-01A-01 4 0.4383 0.335463 0.000 0.000 0.004 0.572 0.424
#> TCGA-08-0357-01A-01 3 0.4063 0.540050 0.000 0.000 0.708 0.012 0.280
#> TCGA-08-0358-01A-01 5 0.4443 -0.178232 0.000 0.000 0.004 0.472 0.524
#> TCGA-08-0375-01A-01 5 0.5154 0.127887 0.048 0.000 0.372 0.000 0.580
#> TCGA-08-0511-01A-01 3 0.3647 0.580568 0.000 0.004 0.764 0.004 0.228
#> TCGA-08-0514-01A-01 3 0.1843 0.620976 0.000 0.008 0.932 0.008 0.052
#> TCGA-08-0518-01A-01 3 0.4380 0.483123 0.008 0.000 0.616 0.000 0.376
#> TCGA-08-0529-01A-02 3 0.4003 0.542791 0.000 0.000 0.704 0.008 0.288
#> TCGA-08-0531-01A-01 3 0.4161 0.539868 0.000 0.000 0.704 0.016 0.280
#> TCGA-02-0057-01A-01 3 0.1082 0.602461 0.000 0.028 0.964 0.000 0.008
#> TCGA-02-0004-01A-01 2 0.0162 0.880833 0.000 0.996 0.000 0.004 0.000
#> TCGA-02-0006-01B-01 3 0.4403 -0.119806 0.000 0.436 0.560 0.000 0.004
#> TCGA-02-0025-01A-01 2 0.0693 0.875117 0.000 0.980 0.000 0.008 0.012
#> TCGA-02-0033-01A-01 2 0.0880 0.885417 0.000 0.968 0.032 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.3305 0.786031 0.000 0.776 0.224 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.1211 0.884120 0.000 0.960 0.024 0.000 0.016
#> TCGA-02-0051-01A-01 2 0.0579 0.876638 0.000 0.984 0.000 0.008 0.008
#> TCGA-02-0054-01A-01 3 0.3160 0.505381 0.000 0.188 0.808 0.000 0.004
#> TCGA-02-0055-01A-01 2 0.0290 0.879269 0.000 0.992 0.000 0.008 0.000
#> TCGA-02-0059-01A-01 2 0.0693 0.875117 0.000 0.980 0.000 0.008 0.012
#> TCGA-02-0064-01A-01 2 0.3796 0.713111 0.000 0.700 0.300 0.000 0.000
#> TCGA-02-0075-01A-01 3 0.3561 0.418635 0.000 0.260 0.740 0.000 0.000
#> TCGA-02-0079-01A-03 2 0.4624 0.617611 0.000 0.740 0.000 0.096 0.164
#> TCGA-02-0085-01A-01 2 0.4029 0.690187 0.000 0.680 0.316 0.000 0.004
#> TCGA-02-0086-01A-01 2 0.0609 0.885149 0.000 0.980 0.020 0.000 0.000
#> TCGA-02-0099-01A-01 3 0.1282 0.599232 0.000 0.044 0.952 0.004 0.000
#> TCGA-02-0106-01A-01 2 0.2127 0.863616 0.000 0.892 0.108 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0162 0.880833 0.000 0.996 0.000 0.004 0.000
#> TCGA-02-0111-01A-01 2 0.0693 0.875117 0.000 0.980 0.000 0.008 0.012
#> TCGA-02-0326-01A-01 5 0.4415 -0.114370 0.000 0.000 0.004 0.444 0.552
#> TCGA-02-0337-01A-01 2 0.4484 0.696292 0.000 0.668 0.308 0.000 0.024
#> TCGA-06-0122-01A-01 3 0.1740 0.620180 0.000 0.012 0.932 0.000 0.056
#> TCGA-06-0124-01A-01 3 0.4171 0.047387 0.000 0.396 0.604 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0794 0.885290 0.000 0.972 0.028 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0290 0.879269 0.000 0.992 0.000 0.008 0.000
#> TCGA-06-0143-01A-01 3 0.1809 0.619484 0.000 0.012 0.928 0.000 0.060
#> TCGA-06-0147-01A-01 2 0.0880 0.885417 0.000 0.968 0.032 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.4309 0.700167 0.000 0.676 0.308 0.000 0.016
#> TCGA-06-0152-01A-02 4 0.4276 0.417752 0.000 0.000 0.004 0.616 0.380
#> TCGA-06-0154-01A-02 2 0.3774 0.716929 0.000 0.704 0.296 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0963 0.885471 0.000 0.964 0.036 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.1410 0.589771 0.000 0.060 0.940 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.3177 0.797218 0.000 0.792 0.208 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.0613 0.881041 0.000 0.984 0.004 0.008 0.004
#> TCGA-06-0189-01A-05 2 0.0693 0.875117 0.000 0.980 0.000 0.008 0.012
#> TCGA-06-0190-01A-01 2 0.3305 0.786031 0.000 0.776 0.224 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0162 0.880833 0.000 0.996 0.000 0.004 0.000
#> TCGA-06-0197-01A-02 2 0.0290 0.879269 0.000 0.992 0.000 0.008 0.000
#> TCGA-06-0210-01A-01 2 0.3949 0.710970 0.000 0.696 0.300 0.000 0.004
#> TCGA-06-0397-01A-01 2 0.4114 0.595014 0.000 0.624 0.376 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.1043 0.885496 0.000 0.960 0.040 0.000 0.000
#> TCGA-06-0412-01A-01 3 0.4415 -0.140766 0.000 0.444 0.552 0.000 0.004
#> TCGA-06-0644-01A-02 2 0.0162 0.880833 0.000 0.996 0.000 0.004 0.000
#> TCGA-06-0645-01A-01 2 0.1608 0.880483 0.000 0.928 0.072 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.1608 0.880483 0.000 0.928 0.072 0.000 0.000
#> TCGA-08-0352-01A-01 3 0.4135 0.205896 0.000 0.340 0.656 0.000 0.004
#> TCGA-08-0360-01A-01 2 0.1608 0.880483 0.000 0.928 0.072 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.0912 0.869527 0.000 0.972 0.000 0.016 0.012
#> TCGA-08-0392-01A-01 2 0.2771 0.753986 0.000 0.860 0.000 0.128 0.012
#> TCGA-08-0509-01A-01 2 0.1544 0.881391 0.000 0.932 0.068 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.3774 0.343678 0.000 0.296 0.704 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.1608 0.880483 0.000 0.928 0.072 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.1341 0.883051 0.000 0.944 0.056 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.4238 0.610826 0.000 0.628 0.368 0.000 0.004
#> TCGA-12-0620-01A-01 2 0.2302 0.877279 0.000 0.916 0.048 0.016 0.020
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.5440 0.68481 0.680 0.000 0.104 0.000 0.128 0.088
#> TCGA-02-0010-01A-01 1 0.0000 0.84077 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.2230 0.80237 0.892 0.000 0.000 0.000 0.084 0.024
#> TCGA-02-0014-01A-01 1 0.0000 0.84077 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.84077 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.84077 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.84077 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.1760 0.82423 0.928 0.000 0.048 0.000 0.004 0.020
#> TCGA-02-0047-01A-01 6 0.5449 -0.26159 0.000 0.000 0.424 0.000 0.120 0.456
#> TCGA-02-0048-01A-01 1 0.5448 0.66393 0.668 0.000 0.172 0.000 0.076 0.084
#> TCGA-02-0060-01A-01 5 0.3569 0.61563 0.008 0.000 0.164 0.000 0.792 0.036
#> TCGA-02-0069-01A-01 1 0.0000 0.84077 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.1007 0.82964 0.956 0.000 0.044 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 5 0.4650 0.26828 0.416 0.000 0.028 0.000 0.548 0.008
#> TCGA-02-0084-01A-03 5 0.3883 0.50643 0.000 0.000 0.028 0.004 0.728 0.240
#> TCGA-02-0087-01A-01 5 0.2592 0.62387 0.000 0.000 0.116 0.004 0.864 0.016
#> TCGA-02-0104-01A-01 1 0.7081 0.29486 0.448 0.000 0.012 0.296 0.168 0.076
#> TCGA-02-0114-01A-01 1 0.0748 0.83832 0.976 0.000 0.004 0.000 0.004 0.016
#> TCGA-02-0281-01A-01 1 0.0000 0.84077 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.4125 0.58192 0.000 0.000 0.128 0.000 0.748 0.124
#> TCGA-02-0325-01A-01 5 0.5141 0.56263 0.076 0.000 0.344 0.000 0.572 0.008
#> TCGA-02-0338-01A-01 1 0.0000 0.84077 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.84077 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 5 0.4678 0.25244 0.420 0.000 0.024 0.000 0.544 0.012
#> TCGA-02-0439-01A-01 5 0.3857 0.54954 0.000 0.000 0.152 0.000 0.768 0.080
#> TCGA-02-0440-01A-01 1 0.5849 0.63805 0.636 0.000 0.132 0.000 0.144 0.088
#> TCGA-02-0446-01A-01 6 0.5385 -0.25853 0.000 0.000 0.420 0.000 0.112 0.468
#> TCGA-06-0128-01A-01 4 0.7342 -0.02741 0.000 0.000 0.196 0.348 0.328 0.128
#> TCGA-06-0129-01A-01 1 0.0146 0.84029 0.996 0.000 0.004 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.3445 0.53475 0.744 0.000 0.012 0.000 0.244 0.000
#> TCGA-06-0156-01A-01 3 0.5737 0.45267 0.000 0.000 0.512 0.000 0.216 0.272
#> TCGA-06-0166-01A-01 3 0.5758 0.38461 0.000 0.000 0.456 0.000 0.176 0.368
#> TCGA-06-0174-01A-01 1 0.5264 0.69871 0.696 0.000 0.088 0.000 0.128 0.088
#> TCGA-06-0177-01A-01 5 0.6155 0.07154 0.364 0.000 0.112 0.000 0.480 0.044
#> TCGA-06-0238-01A-02 4 0.3364 0.67941 0.000 0.008 0.000 0.828 0.096 0.068
#> TCGA-06-0241-01A-02 1 0.5918 0.62726 0.628 0.000 0.140 0.000 0.144 0.088
#> TCGA-06-0410-01A-01 4 0.5562 0.48327 0.004 0.000 0.056 0.660 0.180 0.100
#> TCGA-06-0413-01A-01 1 0.0000 0.84077 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.5849 0.63805 0.636 0.000 0.132 0.000 0.144 0.088
#> TCGA-06-0646-01A-01 6 0.5421 -0.28394 0.000 0.000 0.432 0.000 0.116 0.452
#> TCGA-06-0648-01A-01 5 0.4616 0.54172 0.156 0.000 0.068 0.000 0.736 0.040
#> TCGA-08-0245-01A-01 1 0.4824 0.72960 0.736 0.000 0.072 0.000 0.104 0.088
#> TCGA-08-0344-01A-01 1 0.2052 0.81845 0.912 0.000 0.004 0.000 0.056 0.028
#> TCGA-08-0347-01A-01 3 0.5547 0.42532 0.000 0.000 0.508 0.000 0.148 0.344
#> TCGA-08-0348-01A-01 5 0.5964 -0.19093 0.004 0.000 0.400 0.000 0.408 0.188
#> TCGA-08-0350-01A-01 5 0.2612 0.62814 0.008 0.000 0.108 0.000 0.868 0.016
#> TCGA-08-0353-01A-01 3 0.3872 0.54550 0.036 0.000 0.800 0.000 0.048 0.116
#> TCGA-08-0359-01A-01 5 0.4709 0.45122 0.000 0.000 0.188 0.000 0.680 0.132
#> TCGA-08-0385-01A-01 5 0.4544 0.49188 0.208 0.000 0.036 0.000 0.716 0.040
#> TCGA-08-0517-01A-01 1 0.5668 0.66049 0.656 0.000 0.140 0.000 0.116 0.088
#> TCGA-08-0524-01A-01 1 0.0000 0.84077 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 4 0.4874 0.53895 0.000 0.000 0.016 0.680 0.216 0.088
#> TCGA-12-0618-01A-01 1 0.2380 0.81247 0.892 0.000 0.004 0.000 0.068 0.036
#> TCGA-02-0089-01A-01 6 0.4634 0.57523 0.000 0.144 0.072 0.036 0.004 0.744
#> TCGA-02-0113-01A-01 4 0.6141 0.11808 0.000 0.004 0.212 0.484 0.008 0.292
#> TCGA-02-0115-01A-01 6 0.6272 0.28191 0.000 0.016 0.164 0.260 0.020 0.540
#> TCGA-02-0451-01A-01 6 0.4237 0.58794 0.000 0.084 0.132 0.020 0.000 0.764
#> TCGA-06-0132-01A-02 4 0.5329 0.20297 0.000 0.432 0.000 0.488 0.016 0.064
#> TCGA-06-0133-01A-02 4 0.0436 0.74899 0.000 0.004 0.000 0.988 0.004 0.004
#> TCGA-06-0138-01A-02 4 0.0000 0.74955 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0160-01A-01 5 0.4766 0.35501 0.000 0.000 0.028 0.296 0.644 0.032
#> TCGA-06-0162-01A-01 4 0.2213 0.69930 0.000 0.100 0.000 0.888 0.008 0.004
#> TCGA-06-0167-01A-01 5 0.4653 0.34071 0.000 0.000 0.020 0.304 0.644 0.032
#> TCGA-06-0171-01A-02 4 0.0146 0.75008 0.000 0.004 0.000 0.996 0.000 0.000
#> TCGA-06-0173-01A-01 6 0.5392 -0.30622 0.000 0.000 0.440 0.000 0.112 0.448
#> TCGA-06-0179-01A-02 4 0.1251 0.74047 0.000 0.024 0.000 0.956 0.008 0.012
#> TCGA-06-0182-01A-01 4 0.0146 0.75008 0.000 0.004 0.000 0.996 0.000 0.000
#> TCGA-06-0185-01A-01 4 0.0291 0.74868 0.000 0.000 0.000 0.992 0.004 0.004
#> TCGA-06-0195-01B-01 4 0.3544 0.62683 0.000 0.000 0.008 0.804 0.140 0.048
#> TCGA-06-0208-01B-01 4 0.0146 0.75008 0.000 0.004 0.000 0.996 0.000 0.000
#> TCGA-06-0214-01A-02 6 0.5311 0.18048 0.000 0.004 0.292 0.008 0.096 0.600
#> TCGA-06-0219-01A-01 4 0.0146 0.75008 0.000 0.004 0.000 0.996 0.000 0.000
#> TCGA-06-0221-01A-01 4 0.0146 0.74917 0.000 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0237-01A-02 4 0.0000 0.74955 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0240-01A-02 4 0.0458 0.74816 0.000 0.000 0.000 0.984 0.000 0.016
#> TCGA-08-0349-01A-01 4 0.5887 0.33261 0.000 0.000 0.020 0.520 0.136 0.324
#> TCGA-08-0380-01A-01 4 0.4868 0.46913 0.000 0.332 0.000 0.608 0.016 0.044
#> TCGA-08-0386-01A-01 3 0.2826 0.64291 0.000 0.000 0.844 0.000 0.028 0.128
#> TCGA-08-0520-01A-01 4 0.1088 0.74136 0.000 0.000 0.000 0.960 0.024 0.016
#> TCGA-02-0007-01A-01 3 0.1719 0.64708 0.000 0.000 0.924 0.000 0.016 0.060
#> TCGA-02-0009-01A-01 3 0.1296 0.62674 0.032 0.000 0.952 0.000 0.012 0.004
#> TCGA-02-0016-01A-01 3 0.2491 0.48789 0.000 0.000 0.836 0.000 0.164 0.000
#> TCGA-02-0021-01A-01 3 0.0790 0.66494 0.000 0.000 0.968 0.000 0.000 0.032
#> TCGA-02-0023-01B-01 5 0.6006 0.00938 0.000 0.020 0.000 0.396 0.448 0.136
#> TCGA-02-0027-01A-01 3 0.1265 0.64184 0.000 0.000 0.948 0.000 0.044 0.008
#> TCGA-02-0038-01A-01 3 0.5216 0.26478 0.000 0.000 0.484 0.000 0.092 0.424
#> TCGA-02-0043-01A-01 3 0.2118 0.56249 0.104 0.000 0.888 0.000 0.008 0.000
#> TCGA-02-0070-01A-01 3 0.3123 0.64616 0.000 0.000 0.836 0.000 0.088 0.076
#> TCGA-02-0102-01A-01 3 0.0881 0.64732 0.008 0.000 0.972 0.000 0.008 0.012
#> TCGA-02-0260-01A-03 5 0.6519 0.55669 0.184 0.000 0.288 0.000 0.480 0.048
#> TCGA-02-0269-01B-01 5 0.4902 0.54069 0.004 0.000 0.364 0.000 0.572 0.060
#> TCGA-02-0285-01A-01 3 0.5319 0.28242 0.000 0.000 0.476 0.000 0.104 0.420
#> TCGA-02-0289-01A-01 5 0.4798 0.53155 0.000 0.000 0.376 0.000 0.564 0.060
#> TCGA-02-0290-01A-01 4 0.5929 0.48266 0.000 0.076 0.000 0.620 0.172 0.132
#> TCGA-02-0317-01A-01 5 0.5262 0.56895 0.000 0.004 0.268 0.004 0.612 0.112
#> TCGA-02-0333-01A-02 5 0.4788 0.53473 0.000 0.000 0.372 0.000 0.568 0.060
#> TCGA-02-0422-01A-01 3 0.4939 0.51208 0.000 0.000 0.612 0.000 0.096 0.292
#> TCGA-02-0430-01A-01 3 0.1152 0.66812 0.000 0.000 0.952 0.000 0.004 0.044
#> TCGA-06-0125-01A-01 3 0.1745 0.59420 0.068 0.000 0.920 0.000 0.012 0.000
#> TCGA-06-0126-01A-01 3 0.1845 0.59432 0.052 0.000 0.920 0.000 0.028 0.000
#> TCGA-06-0137-01A-03 3 0.1411 0.61592 0.000 0.000 0.936 0.000 0.060 0.004
#> TCGA-06-0145-01A-04 3 0.4863 0.45339 0.000 0.000 0.624 0.000 0.092 0.284
#> TCGA-06-0148-01A-01 3 0.3618 0.37333 0.000 0.000 0.776 0.000 0.176 0.048
#> TCGA-06-0187-01A-01 3 0.5216 0.26478 0.000 0.000 0.484 0.000 0.092 0.424
#> TCGA-06-0211-01B-01 3 0.3930 0.62416 0.000 0.000 0.764 0.000 0.092 0.144
#> TCGA-06-0402-01A-01 3 0.1152 0.66891 0.000 0.000 0.952 0.000 0.004 0.044
#> TCGA-08-0246-01A-01 6 0.5319 0.50356 0.000 0.076 0.188 0.000 0.064 0.672
#> TCGA-08-0354-01A-01 4 0.4212 0.66013 0.000 0.084 0.000 0.784 0.052 0.080
#> TCGA-08-0355-01A-01 4 0.6000 0.09069 0.000 0.020 0.000 0.456 0.388 0.136
#> TCGA-08-0357-01A-01 3 0.5042 0.51011 0.000 0.000 0.604 0.000 0.108 0.288
#> TCGA-08-0358-01A-01 5 0.5499 0.28535 0.000 0.012 0.000 0.284 0.580 0.124
#> TCGA-08-0375-01A-01 3 0.2956 0.49253 0.028 0.000 0.856 0.000 0.100 0.016
#> TCGA-08-0511-01A-01 3 0.4827 0.52610 0.000 0.000 0.632 0.000 0.092 0.276
#> TCGA-08-0514-01A-01 3 0.5213 0.26731 0.000 0.000 0.488 0.000 0.092 0.420
#> TCGA-08-0518-01A-01 3 0.0547 0.65960 0.000 0.000 0.980 0.000 0.000 0.020
#> TCGA-08-0529-01A-02 3 0.4662 0.56737 0.000 0.000 0.668 0.000 0.096 0.236
#> TCGA-08-0531-01A-01 3 0.4727 0.56560 0.000 0.000 0.660 0.000 0.100 0.240
#> TCGA-02-0057-01A-01 6 0.4945 0.30887 0.000 0.004 0.292 0.000 0.084 0.620
#> TCGA-02-0004-01A-01 2 0.0547 0.77464 0.000 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0006-01B-01 6 0.4085 0.59054 0.000 0.156 0.096 0.000 0.000 0.748
#> TCGA-02-0025-01A-01 2 0.0622 0.76335 0.000 0.980 0.000 0.000 0.012 0.008
#> TCGA-02-0033-01A-01 2 0.2848 0.76236 0.000 0.816 0.000 0.000 0.008 0.176
#> TCGA-02-0034-01A-01 2 0.4177 0.36858 0.000 0.520 0.000 0.000 0.012 0.468
#> TCGA-02-0039-01A-01 2 0.3460 0.72920 0.000 0.760 0.000 0.000 0.020 0.220
#> TCGA-02-0051-01A-01 2 0.0146 0.76637 0.000 0.996 0.000 0.000 0.004 0.000
#> TCGA-02-0054-01A-01 6 0.3923 0.55434 0.000 0.060 0.192 0.000 0.000 0.748
#> TCGA-02-0055-01A-01 2 0.0547 0.77464 0.000 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0059-01A-01 2 0.0260 0.76467 0.000 0.992 0.000 0.000 0.008 0.000
#> TCGA-02-0064-01A-01 6 0.4387 0.10368 0.000 0.392 0.016 0.000 0.008 0.584
#> TCGA-02-0075-01A-01 6 0.4702 0.54219 0.000 0.076 0.260 0.000 0.004 0.660
#> TCGA-02-0079-01A-03 2 0.5881 0.30811 0.000 0.608 0.000 0.056 0.208 0.128
#> TCGA-02-0085-01A-01 6 0.3911 0.17106 0.000 0.368 0.000 0.000 0.008 0.624
#> TCGA-02-0086-01A-01 2 0.2902 0.75981 0.000 0.800 0.000 0.000 0.004 0.196
#> TCGA-02-0099-01A-01 6 0.5137 0.13540 0.000 0.004 0.348 0.000 0.084 0.564
#> TCGA-02-0106-01A-01 2 0.3619 0.67015 0.000 0.680 0.000 0.000 0.004 0.316
#> TCGA-02-0107-01A-01 2 0.1219 0.77763 0.000 0.948 0.000 0.000 0.004 0.048
#> TCGA-02-0111-01A-01 2 0.0363 0.76496 0.000 0.988 0.000 0.000 0.012 0.000
#> TCGA-02-0326-01A-01 5 0.5566 0.31197 0.000 0.012 0.004 0.268 0.592 0.124
#> TCGA-02-0337-01A-01 6 0.4443 0.08873 0.000 0.368 0.000 0.000 0.036 0.596
#> TCGA-06-0122-01A-01 3 0.5151 0.03989 0.000 0.000 0.472 0.000 0.084 0.444
#> TCGA-06-0124-01A-01 6 0.5078 0.59071 0.000 0.140 0.196 0.000 0.008 0.656
#> TCGA-06-0130-01A-01 2 0.2706 0.76554 0.000 0.832 0.000 0.000 0.008 0.160
#> TCGA-06-0139-01A-01 2 0.0547 0.77464 0.000 0.980 0.000 0.000 0.000 0.020
#> TCGA-06-0143-01A-01 3 0.5151 0.03989 0.000 0.000 0.472 0.000 0.084 0.444
#> TCGA-06-0147-01A-01 2 0.3014 0.76146 0.000 0.804 0.000 0.000 0.012 0.184
#> TCGA-06-0149-01A-05 6 0.4131 0.11825 0.000 0.384 0.000 0.000 0.016 0.600
#> TCGA-06-0152-01A-02 4 0.5896 0.21200 0.000 0.020 0.000 0.508 0.340 0.132
#> TCGA-06-0154-01A-02 6 0.3984 0.10142 0.000 0.396 0.000 0.000 0.008 0.596
#> TCGA-06-0164-01A-01 2 0.3052 0.74993 0.000 0.780 0.000 0.000 0.004 0.216
#> TCGA-06-0175-01A-01 6 0.4935 0.23733 0.000 0.008 0.324 0.000 0.064 0.604
#> TCGA-06-0176-01A-03 2 0.3923 0.57129 0.000 0.620 0.000 0.000 0.008 0.372
#> TCGA-06-0184-01A-01 2 0.2653 0.75902 0.000 0.844 0.000 0.000 0.012 0.144
#> TCGA-06-0189-01A-05 2 0.0260 0.76467 0.000 0.992 0.000 0.000 0.008 0.000
#> TCGA-06-0190-01A-01 2 0.4086 0.38593 0.000 0.528 0.000 0.000 0.008 0.464
#> TCGA-06-0194-01A-01 2 0.0713 0.77610 0.000 0.972 0.000 0.000 0.000 0.028
#> TCGA-06-0197-01A-02 2 0.0603 0.77271 0.000 0.980 0.000 0.000 0.004 0.016
#> TCGA-06-0210-01A-01 6 0.3727 0.12808 0.000 0.388 0.000 0.000 0.000 0.612
#> TCGA-06-0397-01A-01 6 0.4184 0.38405 0.000 0.296 0.028 0.000 0.004 0.672
#> TCGA-06-0409-01A-02 2 0.3670 0.70603 0.000 0.704 0.000 0.000 0.012 0.284
#> TCGA-06-0412-01A-01 6 0.4165 0.58821 0.000 0.160 0.100 0.000 0.000 0.740
#> TCGA-06-0644-01A-02 2 0.0547 0.77464 0.000 0.980 0.000 0.000 0.000 0.020
#> TCGA-06-0645-01A-01 2 0.3887 0.63534 0.000 0.632 0.000 0.000 0.008 0.360
#> TCGA-08-0346-01A-01 2 0.3967 0.63643 0.000 0.632 0.000 0.000 0.012 0.356
#> TCGA-08-0352-01A-01 6 0.4513 0.60414 0.000 0.116 0.152 0.000 0.008 0.724
#> TCGA-08-0360-01A-01 2 0.3940 0.64182 0.000 0.640 0.000 0.000 0.012 0.348
#> TCGA-08-0390-01A-01 2 0.1059 0.75546 0.000 0.964 0.000 0.004 0.016 0.016
#> TCGA-08-0392-01A-01 2 0.1793 0.71280 0.000 0.928 0.000 0.048 0.012 0.012
#> TCGA-08-0509-01A-01 2 0.3927 0.64708 0.000 0.644 0.000 0.000 0.012 0.344
#> TCGA-08-0510-01A-01 6 0.4435 0.59083 0.000 0.100 0.176 0.000 0.004 0.720
#> TCGA-08-0512-01A-01 2 0.3912 0.65173 0.000 0.648 0.000 0.000 0.012 0.340
#> TCGA-08-0522-01A-01 2 0.3398 0.72675 0.000 0.740 0.000 0.000 0.008 0.252
#> TCGA-12-0619-01A-01 6 0.4153 0.26778 0.000 0.340 0.012 0.000 0.008 0.640
#> TCGA-12-0620-01A-01 2 0.5123 0.57751 0.000 0.616 0.000 0.024 0.060 0.300
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> ATC:kmeans 167 5.56e-23 2
#> ATC:kmeans 137 8.71e-34 3
#> ATC:kmeans 170 6.65e-52 4
#> ATC:kmeans 126 3.67e-40 5
#> ATC:kmeans 119 5.32e-48 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "skmeans"]
# you can also extract it by
# res = res_list["ATC:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.970 0.988 0.5030 0.497 0.497
#> 3 3 0.925 0.916 0.965 0.2692 0.809 0.634
#> 4 4 0.942 0.904 0.951 0.1474 0.845 0.602
#> 5 5 0.798 0.694 0.860 0.0643 0.929 0.750
#> 6 6 0.749 0.593 0.752 0.0408 0.924 0.697
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.9815 0.281 0.580 0.420
#> TCGA-02-0048-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0084-01A-03 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0087-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0104-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0325-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.7528 0.724 0.784 0.216
#> TCGA-06-0128-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0166-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0174-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0238-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0646-01A-01 1 0.7883 0.692 0.764 0.236
#> TCGA-06-0648-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0348-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0353-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0115-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0138-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0171-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0173-01A-01 1 0.1184 0.969 0.984 0.016
#> TCGA-06-0179-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0185-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0221-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0237-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0240-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0349-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0520-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0007-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0009-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0016-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0021-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0023-01B-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0038-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0043-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0070-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0102-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0260-01A-03 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0269-01B-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0285-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0289-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0290-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0317-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0333-01A-02 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0422-01A-01 1 0.4690 0.881 0.900 0.100
#> TCGA-02-0430-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0125-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0126-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0137-01A-03 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0145-01A-04 1 0.0376 0.980 0.996 0.004
#> TCGA-06-0148-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0187-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0211-01B-01 1 0.0000 0.984 1.000 0.000
#> TCGA-06-0402-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0246-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0357-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0358-01A-01 1 0.9286 0.478 0.656 0.344
#> TCGA-08-0375-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0511-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0514-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0518-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0529-01A-02 1 0.0000 0.984 1.000 0.000
#> TCGA-08-0531-01A-01 1 0.0000 0.984 1.000 0.000
#> TCGA-02-0057-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-02-0337-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.9460 0.418 0.364 0.636
#> TCGA-06-0124-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.9608 0.366 0.384 0.616
#> TCGA-06-0147-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.991 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.991 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.991 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 2 0.4796 0.6863 0.220 0.780 0.000
#> TCGA-02-0048-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0084-01A-03 2 0.3551 0.8319 0.000 0.868 0.132
#> TCGA-02-0087-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0104-01A-01 3 0.6180 0.3851 0.416 0.000 0.584
#> TCGA-02-0114-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.5733 0.5808 0.324 0.000 0.676
#> TCGA-02-0325-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0439-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 2 0.6235 0.2175 0.436 0.564 0.000
#> TCGA-06-0128-01A-01 1 0.0237 0.9735 0.996 0.000 0.004
#> TCGA-06-0129-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-06-0166-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-06-0174-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-06-0238-01A-02 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0241-01A-02 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-06-0410-01A-01 3 0.5216 0.6756 0.260 0.000 0.740
#> TCGA-06-0413-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 1 0.6140 0.3112 0.596 0.404 0.000
#> TCGA-06-0648-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0347-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0348-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0350-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0353-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0359-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 3 0.0237 0.9053 0.004 0.000 0.996
#> TCGA-12-0618-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0113-01A-01 3 0.0592 0.9020 0.000 0.012 0.988
#> TCGA-02-0115-01A-01 2 0.3941 0.8015 0.000 0.844 0.156
#> TCGA-02-0451-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0132-01A-02 2 0.4555 0.7374 0.000 0.800 0.200
#> TCGA-06-0133-01A-02 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0138-01A-02 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0160-01A-01 3 0.5733 0.5807 0.324 0.000 0.676
#> TCGA-06-0162-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0167-01A-01 3 0.4235 0.7725 0.176 0.000 0.824
#> TCGA-06-0171-01A-02 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0173-01A-01 1 0.5497 0.5749 0.708 0.292 0.000
#> TCGA-06-0179-01A-02 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0182-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0185-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0195-01B-01 3 0.0237 0.9053 0.004 0.000 0.996
#> TCGA-06-0208-01B-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0214-01A-02 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0219-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0221-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0237-01A-02 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0240-01A-02 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-08-0349-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-08-0380-01A-01 3 0.5968 0.4054 0.000 0.364 0.636
#> TCGA-08-0386-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0520-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-02-0007-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-02-0009-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-02-0016-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-02-0021-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-02-0023-01B-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-02-0027-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-02-0038-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-02-0043-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-02-0070-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-02-0102-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-02-0260-01A-03 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-02-0269-01B-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-02-0285-01A-01 2 0.6180 0.2918 0.000 0.584 0.416
#> TCGA-02-0289-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-02-0290-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-02-0317-01A-01 3 0.5706 0.5827 0.320 0.000 0.680
#> TCGA-02-0333-01A-02 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-02-0422-01A-01 1 0.4409 0.7549 0.824 0.172 0.004
#> TCGA-02-0430-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-06-0125-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-06-0126-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-06-0137-01A-03 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-06-0145-01A-04 1 0.6264 0.3770 0.616 0.380 0.004
#> TCGA-06-0148-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-06-0187-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-06-0211-01B-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-06-0402-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-08-0246-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-08-0354-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-08-0355-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-08-0357-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-08-0358-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-08-0375-01A-01 1 0.0000 0.9767 1.000 0.000 0.000
#> TCGA-08-0511-01A-01 1 0.0661 0.9677 0.988 0.008 0.004
#> TCGA-08-0514-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-08-0518-01A-01 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-08-0529-01A-02 1 0.0237 0.9752 0.996 0.000 0.004
#> TCGA-08-0531-01A-01 3 0.6309 0.0553 0.500 0.000 0.500
#> TCGA-02-0057-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-02-0004-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0054-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-02-0075-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-02-0079-01A-03 3 0.4974 0.6460 0.000 0.236 0.764
#> TCGA-02-0085-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0086-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0099-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-02-0106-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-02-0326-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-02-0337-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0122-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-06-0124-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-06-0130-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0143-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-06-0147-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0152-01A-02 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-06-0154-01A-02 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-06-0176-01A-03 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0412-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-08-0352-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.0592 0.9613 0.000 0.988 0.012
#> TCGA-08-0392-01A-01 3 0.0237 0.9078 0.000 0.004 0.996
#> TCGA-08-0509-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 2 0.0237 0.9690 0.000 0.996 0.004
#> TCGA-08-0512-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9713 0.000 1.000 0.000
#> TCGA-12-0620-01A-01 2 0.0592 0.9613 0.000 0.988 0.012
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0188 0.936 0.996 0.000 0.004 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0188 0.936 0.996 0.000 0.004 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 1 0.4163 0.718 0.792 0.188 0.020 0.000
#> TCGA-02-0048-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.1637 0.917 0.940 0.000 0.060 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.1716 0.914 0.936 0.000 0.064 0.000
#> TCGA-02-0084-01A-03 2 0.5993 0.446 0.000 0.628 0.064 0.308
#> TCGA-02-0087-01A-01 1 0.1716 0.914 0.936 0.000 0.064 0.000
#> TCGA-02-0104-01A-01 1 0.1824 0.908 0.936 0.000 0.004 0.060
#> TCGA-02-0114-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0188 0.936 0.996 0.000 0.004 0.000
#> TCGA-02-0321-01A-01 4 0.6296 0.265 0.388 0.000 0.064 0.548
#> TCGA-02-0325-01A-01 1 0.3569 0.786 0.804 0.000 0.196 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0469 0.935 0.988 0.000 0.012 0.000
#> TCGA-02-0432-01A-02 1 0.1637 0.917 0.940 0.000 0.060 0.000
#> TCGA-02-0439-01A-01 1 0.1716 0.914 0.936 0.000 0.064 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.4706 0.630 0.732 0.248 0.020 0.000
#> TCGA-06-0128-01A-01 1 0.0592 0.933 0.984 0.000 0.000 0.016
#> TCGA-06-0129-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.1557 0.919 0.944 0.000 0.056 0.000
#> TCGA-06-0156-01A-01 1 0.0469 0.932 0.988 0.000 0.012 0.000
#> TCGA-06-0166-01A-01 1 0.0592 0.930 0.984 0.000 0.016 0.000
#> TCGA-06-0174-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.1211 0.925 0.960 0.000 0.040 0.000
#> TCGA-06-0238-01A-02 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.1792 0.903 0.932 0.000 0.000 0.068
#> TCGA-06-0413-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 1 0.4542 0.660 0.752 0.228 0.020 0.000
#> TCGA-06-0648-01A-01 1 0.1716 0.914 0.936 0.000 0.064 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0469 0.935 0.988 0.000 0.012 0.000
#> TCGA-08-0347-01A-01 1 0.1940 0.911 0.924 0.000 0.076 0.000
#> TCGA-08-0348-01A-01 1 0.0336 0.936 0.992 0.000 0.008 0.000
#> TCGA-08-0350-01A-01 1 0.1716 0.914 0.936 0.000 0.064 0.000
#> TCGA-08-0353-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-08-0359-01A-01 1 0.1940 0.911 0.924 0.000 0.076 0.000
#> TCGA-08-0385-01A-01 1 0.1716 0.914 0.936 0.000 0.064 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.937 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-12-0618-01A-01 1 0.0469 0.935 0.988 0.000 0.012 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0113-01A-01 4 0.0469 0.949 0.000 0.012 0.000 0.988
#> TCGA-02-0115-01A-01 2 0.3569 0.755 0.000 0.804 0.000 0.196
#> TCGA-02-0451-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0132-01A-02 2 0.4888 0.310 0.000 0.588 0.000 0.412
#> TCGA-06-0133-01A-02 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.4121 0.761 0.796 0.000 0.020 0.184
#> TCGA-06-0162-01A-01 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.5488 0.165 0.532 0.000 0.016 0.452
#> TCGA-06-0171-01A-02 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 1 0.2174 0.886 0.928 0.052 0.020 0.000
#> TCGA-06-0179-01A-02 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0195-01B-01 4 0.0921 0.935 0.028 0.000 0.000 0.972
#> TCGA-06-0208-01B-01 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.1610 0.943 0.000 0.952 0.016 0.032
#> TCGA-06-0219-01A-01 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-08-0349-01A-01 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 4 0.3837 0.691 0.000 0.224 0.000 0.776
#> TCGA-08-0386-01A-01 1 0.4761 0.349 0.628 0.000 0.372 0.000
#> TCGA-08-0520-01A-01 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 3 0.2647 0.884 0.120 0.000 0.880 0.000
#> TCGA-02-0009-01A-01 3 0.2081 0.909 0.084 0.000 0.916 0.000
#> TCGA-02-0016-01A-01 3 0.0817 0.902 0.024 0.000 0.976 0.000
#> TCGA-02-0021-01A-01 3 0.2081 0.909 0.084 0.000 0.916 0.000
#> TCGA-02-0023-01B-01 4 0.1389 0.931 0.000 0.000 0.048 0.952
#> TCGA-02-0027-01A-01 3 0.4697 0.531 0.356 0.000 0.644 0.000
#> TCGA-02-0038-01A-01 2 0.1209 0.951 0.004 0.964 0.032 0.000
#> TCGA-02-0043-01A-01 3 0.2081 0.909 0.084 0.000 0.916 0.000
#> TCGA-02-0070-01A-01 3 0.0707 0.900 0.020 0.000 0.980 0.000
#> TCGA-02-0102-01A-01 3 0.2081 0.909 0.084 0.000 0.916 0.000
#> TCGA-02-0260-01A-03 3 0.0707 0.900 0.020 0.000 0.980 0.000
#> TCGA-02-0269-01B-01 3 0.0707 0.900 0.020 0.000 0.980 0.000
#> TCGA-02-0285-01A-01 3 0.3634 0.808 0.000 0.048 0.856 0.096
#> TCGA-02-0289-01A-01 3 0.0707 0.900 0.020 0.000 0.980 0.000
#> TCGA-02-0290-01A-01 4 0.0188 0.955 0.000 0.000 0.004 0.996
#> TCGA-02-0317-01A-01 3 0.0779 0.898 0.016 0.000 0.980 0.004
#> TCGA-02-0333-01A-02 3 0.0707 0.900 0.020 0.000 0.980 0.000
#> TCGA-02-0422-01A-01 3 0.0779 0.900 0.016 0.004 0.980 0.000
#> TCGA-02-0430-01A-01 3 0.2081 0.909 0.084 0.000 0.916 0.000
#> TCGA-06-0125-01A-01 3 0.2081 0.909 0.084 0.000 0.916 0.000
#> TCGA-06-0126-01A-01 3 0.2081 0.909 0.084 0.000 0.916 0.000
#> TCGA-06-0137-01A-03 3 0.1637 0.909 0.060 0.000 0.940 0.000
#> TCGA-06-0145-01A-04 3 0.1824 0.904 0.060 0.004 0.936 0.000
#> TCGA-06-0148-01A-01 3 0.0707 0.900 0.020 0.000 0.980 0.000
#> TCGA-06-0187-01A-01 3 0.4699 0.545 0.004 0.320 0.676 0.000
#> TCGA-06-0211-01B-01 3 0.2081 0.909 0.084 0.000 0.916 0.000
#> TCGA-06-0402-01A-01 3 0.2081 0.909 0.084 0.000 0.916 0.000
#> TCGA-08-0246-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-08-0354-01A-01 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> TCGA-08-0355-01A-01 4 0.1389 0.931 0.000 0.000 0.048 0.952
#> TCGA-08-0357-01A-01 3 0.0336 0.896 0.008 0.000 0.992 0.000
#> TCGA-08-0358-01A-01 4 0.1474 0.929 0.000 0.000 0.052 0.948
#> TCGA-08-0375-01A-01 3 0.2345 0.889 0.100 0.000 0.900 0.000
#> TCGA-08-0511-01A-01 3 0.1716 0.904 0.064 0.000 0.936 0.000
#> TCGA-08-0514-01A-01 3 0.1716 0.868 0.000 0.064 0.936 0.000
#> TCGA-08-0518-01A-01 3 0.2081 0.909 0.084 0.000 0.916 0.000
#> TCGA-08-0529-01A-02 3 0.1302 0.906 0.044 0.000 0.956 0.000
#> TCGA-08-0531-01A-01 3 0.2214 0.892 0.028 0.000 0.928 0.044
#> TCGA-02-0057-01A-01 2 0.0336 0.973 0.000 0.992 0.008 0.000
#> TCGA-02-0004-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.0188 0.976 0.000 0.996 0.004 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.0188 0.976 0.000 0.996 0.004 0.000
#> TCGA-02-0075-01A-01 2 0.0336 0.973 0.000 0.992 0.008 0.000
#> TCGA-02-0079-01A-03 4 0.2996 0.883 0.000 0.064 0.044 0.892
#> TCGA-02-0085-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0086-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.0592 0.967 0.000 0.984 0.016 0.000
#> TCGA-02-0106-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-02-0326-01A-01 4 0.1716 0.920 0.000 0.000 0.064 0.936
#> TCGA-02-0337-01A-01 2 0.0188 0.975 0.000 0.996 0.004 0.000
#> TCGA-06-0122-01A-01 3 0.4250 0.628 0.000 0.276 0.724 0.000
#> TCGA-06-0124-01A-01 2 0.0188 0.976 0.000 0.996 0.004 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.4961 0.219 0.000 0.448 0.552 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0152-01A-02 4 0.1302 0.933 0.000 0.000 0.044 0.956
#> TCGA-06-0154-01A-02 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.0336 0.973 0.000 0.992 0.008 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-08-0352-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.1474 0.933 0.000 0.948 0.000 0.052
#> TCGA-08-0392-01A-01 4 0.0592 0.947 0.000 0.016 0.000 0.984
#> TCGA-08-0509-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-08-0510-01A-01 2 0.0336 0.973 0.000 0.992 0.008 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.978 0.000 1.000 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.1661 0.930 0.000 0.944 0.004 0.052
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0510 0.8206 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0014-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 1 0.4709 0.3787 0.584 0.000 0.008 0.008 0.400
#> TCGA-02-0048-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.4074 0.3110 0.636 0.000 0.000 0.000 0.364
#> TCGA-02-0069-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.4273 0.0354 0.552 0.000 0.000 0.000 0.448
#> TCGA-02-0084-01A-03 5 0.3424 0.3646 0.000 0.240 0.000 0.000 0.760
#> TCGA-02-0087-01A-01 5 0.4088 0.3934 0.368 0.000 0.000 0.000 0.632
#> TCGA-02-0104-01A-01 1 0.1043 0.7979 0.960 0.000 0.000 0.040 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.5299 0.4421 0.336 0.000 0.016 0.036 0.612
#> TCGA-02-0325-01A-01 5 0.4256 0.2744 0.436 0.000 0.000 0.000 0.564
#> TCGA-02-0338-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.4074 0.3110 0.636 0.000 0.000 0.000 0.364
#> TCGA-02-0439-01A-01 5 0.4307 0.0676 0.500 0.000 0.000 0.000 0.500
#> TCGA-02-0440-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.4264 0.4074 0.620 0.000 0.004 0.000 0.376
#> TCGA-06-0128-01A-01 1 0.0510 0.8206 0.984 0.000 0.000 0.000 0.016
#> TCGA-06-0129-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.3913 0.4003 0.676 0.000 0.000 0.000 0.324
#> TCGA-06-0156-01A-01 1 0.2329 0.7275 0.876 0.000 0.000 0.000 0.124
#> TCGA-06-0166-01A-01 1 0.2439 0.7276 0.876 0.000 0.004 0.000 0.120
#> TCGA-06-0174-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0880 0.8065 0.968 0.000 0.000 0.000 0.032
#> TCGA-06-0238-01A-02 4 0.2074 0.7253 0.000 0.000 0.000 0.896 0.104
#> TCGA-06-0241-01A-02 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.3242 0.5778 0.784 0.000 0.000 0.216 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 1 0.4264 0.4074 0.620 0.000 0.004 0.000 0.376
#> TCGA-06-0648-01A-01 1 0.4074 0.3101 0.636 0.000 0.000 0.000 0.364
#> TCGA-08-0245-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 1 0.4415 0.2139 0.552 0.000 0.004 0.000 0.444
#> TCGA-08-0348-01A-01 1 0.0963 0.8103 0.964 0.000 0.000 0.000 0.036
#> TCGA-08-0350-01A-01 5 0.4283 0.2260 0.456 0.000 0.000 0.000 0.544
#> TCGA-08-0353-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0359-01A-01 1 0.4015 0.3677 0.652 0.000 0.000 0.000 0.348
#> TCGA-08-0385-01A-01 1 0.3983 0.3660 0.660 0.000 0.000 0.000 0.340
#> TCGA-08-0517-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 4 0.0693 0.8012 0.012 0.000 0.000 0.980 0.008
#> TCGA-12-0618-01A-01 1 0.0000 0.8292 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.2424 0.8068 0.000 0.868 0.000 0.132 0.000
#> TCGA-02-0113-01A-01 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0115-01A-01 4 0.5440 0.5031 0.000 0.252 0.004 0.648 0.096
#> TCGA-02-0451-01A-01 2 0.5041 0.7034 0.000 0.716 0.004 0.132 0.148
#> TCGA-06-0132-01A-02 4 0.4242 0.2962 0.000 0.428 0.000 0.572 0.000
#> TCGA-06-0133-01A-02 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0138-01A-02 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0160-01A-01 1 0.6519 -0.1388 0.448 0.000 0.000 0.200 0.352
#> TCGA-06-0162-01A-01 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0167-01A-01 5 0.6806 0.2351 0.352 0.000 0.000 0.296 0.352
#> TCGA-06-0171-01A-02 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0173-01A-01 1 0.6823 -0.0393 0.384 0.000 0.236 0.004 0.376
#> TCGA-06-0179-01A-02 4 0.0609 0.8019 0.000 0.020 0.000 0.980 0.000
#> TCGA-06-0182-01A-01 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0185-01A-01 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0195-01B-01 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0208-01B-01 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0214-01A-02 4 0.6652 0.2883 0.000 0.196 0.004 0.440 0.360
#> TCGA-06-0219-01A-01 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0221-01A-01 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0237-01A-02 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0240-01A-02 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-08-0349-01A-01 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-08-0380-01A-01 4 0.3932 0.4901 0.000 0.328 0.000 0.672 0.000
#> TCGA-08-0386-01A-01 3 0.4150 0.3269 0.388 0.000 0.612 0.000 0.000
#> TCGA-08-0520-01A-01 4 0.0000 0.8143 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0007-01A-01 3 0.3876 0.4409 0.316 0.000 0.684 0.000 0.000
#> TCGA-02-0009-01A-01 3 0.0162 0.7973 0.004 0.000 0.996 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.1544 0.7518 0.000 0.000 0.932 0.000 0.068
#> TCGA-02-0021-01A-01 3 0.0162 0.7973 0.004 0.000 0.996 0.000 0.000
#> TCGA-02-0023-01B-01 4 0.4283 0.1785 0.000 0.000 0.000 0.544 0.456
#> TCGA-02-0027-01A-01 3 0.3969 0.3917 0.304 0.000 0.692 0.000 0.004
#> TCGA-02-0038-01A-01 3 0.5418 0.4979 0.000 0.068 0.568 0.000 0.364
#> TCGA-02-0043-01A-01 3 0.0162 0.7973 0.004 0.000 0.996 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.3452 0.5298 0.000 0.000 0.756 0.000 0.244
#> TCGA-02-0102-01A-01 3 0.0162 0.7973 0.004 0.000 0.996 0.000 0.000
#> TCGA-02-0260-01A-03 5 0.4473 0.3412 0.008 0.000 0.412 0.000 0.580
#> TCGA-02-0269-01B-01 5 0.4192 0.3532 0.000 0.000 0.404 0.000 0.596
#> TCGA-02-0285-01A-01 3 0.7022 0.1674 0.000 0.196 0.484 0.028 0.292
#> TCGA-02-0289-01A-01 5 0.4201 0.3469 0.000 0.000 0.408 0.000 0.592
#> TCGA-02-0290-01A-01 4 0.3586 0.5503 0.000 0.000 0.000 0.736 0.264
#> TCGA-02-0317-01A-01 5 0.4192 0.3532 0.000 0.000 0.404 0.000 0.596
#> TCGA-02-0333-01A-02 5 0.4192 0.3532 0.000 0.000 0.404 0.000 0.596
#> TCGA-02-0422-01A-01 3 0.0000 0.7969 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.0162 0.7973 0.004 0.000 0.996 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0162 0.7973 0.004 0.000 0.996 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.0162 0.7973 0.004 0.000 0.996 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.0162 0.7956 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0145-01A-04 3 0.3752 0.6196 0.000 0.000 0.708 0.000 0.292
#> TCGA-06-0148-01A-01 3 0.3508 0.5168 0.000 0.000 0.748 0.000 0.252
#> TCGA-06-0187-01A-01 3 0.4354 0.5510 0.000 0.008 0.624 0.000 0.368
#> TCGA-06-0211-01B-01 3 0.1341 0.7646 0.056 0.000 0.944 0.000 0.000
#> TCGA-06-0402-01A-01 3 0.0162 0.7973 0.004 0.000 0.996 0.000 0.000
#> TCGA-08-0246-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0354-01A-01 4 0.0162 0.8123 0.000 0.000 0.000 0.996 0.004
#> TCGA-08-0355-01A-01 4 0.4262 0.2208 0.000 0.000 0.000 0.560 0.440
#> TCGA-08-0357-01A-01 3 0.0000 0.7969 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0358-01A-01 5 0.4227 0.0946 0.000 0.000 0.000 0.420 0.580
#> TCGA-08-0375-01A-01 3 0.3163 0.6436 0.164 0.000 0.824 0.000 0.012
#> TCGA-08-0511-01A-01 3 0.0162 0.7961 0.000 0.000 0.996 0.000 0.004
#> TCGA-08-0514-01A-01 3 0.3003 0.6919 0.000 0.000 0.812 0.000 0.188
#> TCGA-08-0518-01A-01 3 0.0000 0.7969 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.7969 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.7969 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0057-01A-01 2 0.5096 0.6557 0.000 0.656 0.072 0.000 0.272
#> TCGA-02-0004-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.3177 0.7932 0.000 0.792 0.000 0.000 0.208
#> TCGA-02-0025-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0794 0.9213 0.000 0.972 0.000 0.000 0.028
#> TCGA-02-0034-01A-01 2 0.0794 0.9213 0.000 0.972 0.000 0.000 0.028
#> TCGA-02-0039-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0054-01A-01 2 0.2707 0.8487 0.000 0.860 0.008 0.000 0.132
#> TCGA-02-0055-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.3508 0.7528 0.000 0.748 0.000 0.000 0.252
#> TCGA-02-0075-01A-01 2 0.4167 0.7317 0.000 0.724 0.024 0.000 0.252
#> TCGA-02-0079-01A-03 2 0.5942 0.1792 0.000 0.524 0.000 0.116 0.360
#> TCGA-02-0085-01A-01 2 0.0290 0.9252 0.000 0.992 0.000 0.000 0.008
#> TCGA-02-0086-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.4862 0.5866 0.000 0.604 0.032 0.000 0.364
#> TCGA-02-0106-01A-01 2 0.0510 0.9236 0.000 0.984 0.000 0.000 0.016
#> TCGA-02-0107-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0326-01A-01 5 0.4192 0.1325 0.000 0.000 0.000 0.404 0.596
#> TCGA-02-0337-01A-01 2 0.2020 0.8568 0.000 0.900 0.000 0.000 0.100
#> TCGA-06-0122-01A-01 3 0.4088 0.5576 0.000 0.000 0.632 0.000 0.368
#> TCGA-06-0124-01A-01 2 0.3890 0.7424 0.000 0.736 0.012 0.000 0.252
#> TCGA-06-0130-01A-01 2 0.0510 0.9243 0.000 0.984 0.000 0.000 0.016
#> TCGA-06-0139-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.5820 0.4540 0.000 0.100 0.524 0.000 0.376
#> TCGA-06-0147-01A-01 2 0.0404 0.9249 0.000 0.988 0.000 0.000 0.012
#> TCGA-06-0149-01A-05 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0152-01A-02 4 0.4150 0.3401 0.000 0.000 0.000 0.612 0.388
#> TCGA-06-0154-01A-02 2 0.0794 0.9213 0.000 0.972 0.000 0.000 0.028
#> TCGA-06-0164-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.4575 0.6458 0.000 0.648 0.024 0.000 0.328
#> TCGA-06-0176-01A-03 2 0.0703 0.9222 0.000 0.976 0.000 0.000 0.024
#> TCGA-06-0184-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0794 0.9213 0.000 0.972 0.000 0.000 0.028
#> TCGA-06-0194-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0794 0.9213 0.000 0.972 0.000 0.000 0.028
#> TCGA-06-0409-01A-02 2 0.0290 0.9252 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0412-01A-01 2 0.1671 0.8943 0.000 0.924 0.000 0.000 0.076
#> TCGA-06-0644-01A-02 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0290 0.9252 0.000 0.992 0.000 0.000 0.008
#> TCGA-08-0346-01A-01 2 0.0290 0.9252 0.000 0.992 0.000 0.000 0.008
#> TCGA-08-0352-01A-01 2 0.0000 0.9254 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0360-01A-01 2 0.0404 0.9249 0.000 0.988 0.000 0.000 0.012
#> TCGA-08-0390-01A-01 2 0.0703 0.9114 0.000 0.976 0.000 0.024 0.000
#> TCGA-08-0392-01A-01 4 0.4307 0.1153 0.000 0.496 0.000 0.504 0.000
#> TCGA-08-0509-01A-01 2 0.0404 0.9249 0.000 0.988 0.000 0.000 0.012
#> TCGA-08-0510-01A-01 2 0.4080 0.7349 0.000 0.728 0.020 0.000 0.252
#> TCGA-08-0512-01A-01 2 0.0794 0.9213 0.000 0.972 0.000 0.000 0.028
#> TCGA-08-0522-01A-01 2 0.0794 0.9213 0.000 0.972 0.000 0.000 0.028
#> TCGA-12-0619-01A-01 2 0.0794 0.9213 0.000 0.972 0.000 0.000 0.028
#> TCGA-12-0620-01A-01 2 0.0880 0.9073 0.000 0.968 0.000 0.000 0.032
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.0260 0.79378 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-02-0010-01A-01 1 0.0146 0.79448 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-02-0011-01B-01 1 0.3543 0.65279 0.768 0.000 0.000 0.000 0.032 0.200
#> TCGA-02-0014-01A-01 1 0.0000 0.79437 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0146 0.79448 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-02-0026-01B-01 1 0.0937 0.78027 0.960 0.000 0.000 0.000 0.000 0.040
#> TCGA-02-0028-01A-01 1 0.0146 0.79448 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-02-0046-01A-01 1 0.0260 0.79378 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-02-0047-01A-01 6 0.5525 0.33847 0.200 0.000 0.004 0.012 0.164 0.620
#> TCGA-02-0048-01A-01 1 0.0260 0.79378 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-02-0060-01A-01 1 0.5942 0.12395 0.444 0.000 0.000 0.000 0.324 0.232
#> TCGA-02-0069-01A-01 1 0.0146 0.79448 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-02-0074-01A-01 1 0.0260 0.79378 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-02-0080-01A-01 1 0.5975 0.05354 0.420 0.000 0.000 0.000 0.348 0.232
#> TCGA-02-0084-01A-03 5 0.3835 0.36523 0.000 0.048 0.000 0.000 0.748 0.204
#> TCGA-02-0087-01A-01 5 0.5685 0.27520 0.240 0.000 0.000 0.000 0.528 0.232
#> TCGA-02-0104-01A-01 1 0.3233 0.67256 0.828 0.000 0.000 0.132 0.024 0.016
#> TCGA-02-0114-01A-01 1 0.0260 0.79378 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-02-0281-01A-01 1 0.0146 0.79448 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-02-0321-01A-01 5 0.3906 0.47362 0.192 0.000 0.028 0.008 0.764 0.008
#> TCGA-02-0325-01A-01 5 0.6293 0.03258 0.376 0.000 0.012 0.000 0.380 0.232
#> TCGA-02-0338-01A-01 1 0.0146 0.79448 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-02-0339-01A-01 1 0.3053 0.68844 0.812 0.000 0.000 0.000 0.020 0.168
#> TCGA-02-0432-01A-02 1 0.5942 0.12395 0.444 0.000 0.000 0.000 0.324 0.232
#> TCGA-02-0439-01A-01 5 0.5992 0.04601 0.340 0.000 0.000 0.000 0.420 0.240
#> TCGA-02-0440-01A-01 1 0.0260 0.79378 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-02-0446-01A-01 6 0.5518 0.38785 0.316 0.000 0.004 0.000 0.136 0.544
#> TCGA-06-0128-01A-01 1 0.3462 0.71364 0.836 0.000 0.000 0.072 0.056 0.036
#> TCGA-06-0129-01A-01 1 0.0260 0.79445 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-06-0146-01A-01 1 0.5630 0.31915 0.540 0.000 0.000 0.000 0.232 0.228
#> TCGA-06-0156-01A-01 1 0.4243 0.56139 0.736 0.000 0.000 0.000 0.132 0.132
#> TCGA-06-0166-01A-01 1 0.5026 0.42781 0.652 0.000 0.004 0.000 0.140 0.204
#> TCGA-06-0174-01A-01 1 0.0260 0.79378 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-06-0177-01A-01 1 0.3388 0.67142 0.792 0.000 0.000 0.000 0.036 0.172
#> TCGA-06-0238-01A-02 4 0.2964 0.69732 0.000 0.000 0.000 0.792 0.204 0.004
#> TCGA-06-0241-01A-02 1 0.0260 0.79378 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-06-0410-01A-01 1 0.4120 0.47226 0.692 0.000 0.000 0.276 0.024 0.008
#> TCGA-06-0413-01A-01 1 0.0146 0.79448 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-06-0414-01A-01 1 0.0260 0.79378 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-06-0646-01A-01 6 0.5677 0.21833 0.400 0.000 0.004 0.000 0.136 0.460
#> TCGA-06-0648-01A-01 1 0.5778 0.24808 0.504 0.000 0.000 0.000 0.268 0.228
#> TCGA-08-0245-01A-01 1 0.0260 0.79378 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-08-0344-01A-01 1 0.3134 0.68811 0.808 0.000 0.000 0.000 0.024 0.168
#> TCGA-08-0347-01A-01 5 0.6185 0.16770 0.224 0.000 0.008 0.000 0.400 0.368
#> TCGA-08-0348-01A-01 1 0.5173 0.51412 0.616 0.000 0.000 0.000 0.160 0.224
#> TCGA-08-0350-01A-01 5 0.5992 0.02537 0.372 0.000 0.000 0.000 0.396 0.232
#> TCGA-08-0353-01A-01 1 0.0405 0.79193 0.988 0.000 0.004 0.000 0.000 0.008
#> TCGA-08-0359-01A-01 1 0.6058 0.05752 0.384 0.000 0.000 0.000 0.356 0.260
#> TCGA-08-0385-01A-01 1 0.5701 0.29163 0.524 0.000 0.000 0.000 0.248 0.228
#> TCGA-08-0517-01A-01 1 0.0260 0.79378 0.992 0.000 0.000 0.000 0.000 0.008
#> TCGA-08-0524-01A-01 1 0.0146 0.79448 0.996 0.000 0.000 0.000 0.000 0.004
#> TCGA-12-0616-01A-01 4 0.3266 0.74938 0.036 0.000 0.000 0.824 0.132 0.008
#> TCGA-12-0618-01A-01 1 0.2981 0.69674 0.820 0.000 0.000 0.000 0.020 0.160
#> TCGA-02-0089-01A-01 2 0.4697 0.47174 0.000 0.684 0.000 0.172 0.000 0.144
#> TCGA-02-0113-01A-01 4 0.1411 0.84191 0.000 0.004 0.000 0.936 0.000 0.060
#> TCGA-02-0115-01A-01 4 0.5888 0.13128 0.000 0.268 0.000 0.476 0.000 0.256
#> TCGA-02-0451-01A-01 2 0.5643 -0.03066 0.000 0.476 0.000 0.156 0.000 0.368
#> TCGA-06-0132-01A-02 2 0.4602 -0.04473 0.000 0.492 0.000 0.476 0.004 0.028
#> TCGA-06-0133-01A-02 4 0.0000 0.89055 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0138-01A-02 4 0.0000 0.89055 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0160-01A-01 5 0.7469 0.10125 0.312 0.000 0.000 0.136 0.320 0.232
#> TCGA-06-0162-01A-01 4 0.0260 0.88633 0.000 0.008 0.000 0.992 0.000 0.000
#> TCGA-06-0167-01A-01 5 0.7642 0.19677 0.256 0.000 0.000 0.192 0.320 0.232
#> TCGA-06-0171-01A-02 4 0.0000 0.89055 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0173-01A-01 6 0.6334 0.40312 0.276 0.000 0.072 0.000 0.120 0.532
#> TCGA-06-0179-01A-02 4 0.1267 0.83882 0.000 0.060 0.000 0.940 0.000 0.000
#> TCGA-06-0182-01A-01 4 0.0000 0.89055 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0185-01A-01 4 0.0000 0.89055 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0195-01B-01 4 0.0692 0.87826 0.004 0.000 0.000 0.976 0.020 0.000
#> TCGA-06-0208-01B-01 4 0.0000 0.89055 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0214-01A-02 6 0.6672 0.27278 0.000 0.132 0.004 0.284 0.080 0.500
#> TCGA-06-0219-01A-01 4 0.0000 0.89055 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0221-01A-01 4 0.0000 0.89055 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0237-01A-02 4 0.0000 0.89055 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0240-01A-02 4 0.0000 0.89055 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0349-01A-01 4 0.0405 0.88701 0.000 0.000 0.000 0.988 0.008 0.004
#> TCGA-08-0380-01A-01 4 0.4528 0.28842 0.000 0.404 0.000 0.564 0.004 0.028
#> TCGA-08-0386-01A-01 1 0.4093 -0.10482 0.516 0.000 0.476 0.000 0.000 0.008
#> TCGA-08-0520-01A-01 4 0.0547 0.88116 0.000 0.000 0.000 0.980 0.020 0.000
#> TCGA-02-0007-01A-01 3 0.3955 0.30449 0.436 0.000 0.560 0.000 0.000 0.004
#> TCGA-02-0009-01A-01 3 0.0632 0.83453 0.024 0.000 0.976 0.000 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.1010 0.81664 0.004 0.000 0.960 0.000 0.036 0.000
#> TCGA-02-0021-01A-01 3 0.0632 0.83453 0.024 0.000 0.976 0.000 0.000 0.000
#> TCGA-02-0023-01B-01 5 0.4891 0.13979 0.000 0.000 0.016 0.384 0.564 0.036
#> TCGA-02-0027-01A-01 3 0.4008 0.43744 0.308 0.000 0.672 0.000 0.016 0.004
#> TCGA-02-0038-01A-01 6 0.5657 0.30282 0.000 0.020 0.324 0.012 0.076 0.568
#> TCGA-02-0043-01A-01 3 0.0632 0.83453 0.024 0.000 0.976 0.000 0.000 0.000
#> TCGA-02-0070-01A-01 3 0.2994 0.62443 0.000 0.000 0.788 0.000 0.208 0.004
#> TCGA-02-0102-01A-01 3 0.0632 0.83453 0.024 0.000 0.976 0.000 0.000 0.000
#> TCGA-02-0260-01A-03 5 0.5904 0.20519 0.044 0.000 0.392 0.000 0.484 0.080
#> TCGA-02-0269-01B-01 5 0.5035 0.22898 0.004 0.000 0.380 0.000 0.548 0.068
#> TCGA-02-0285-01A-01 5 0.6632 0.22650 0.000 0.192 0.212 0.012 0.532 0.052
#> TCGA-02-0289-01A-01 5 0.4597 0.16646 0.000 0.000 0.412 0.000 0.548 0.040
#> TCGA-02-0290-01A-01 5 0.5049 -0.08550 0.000 0.008 0.008 0.472 0.476 0.036
#> TCGA-02-0317-01A-01 5 0.3615 0.32607 0.000 0.000 0.292 0.000 0.700 0.008
#> TCGA-02-0333-01A-02 5 0.4888 0.22841 0.004 0.000 0.380 0.000 0.560 0.056
#> TCGA-02-0422-01A-01 3 0.2250 0.79431 0.000 0.000 0.896 0.000 0.040 0.064
#> TCGA-02-0430-01A-01 3 0.0632 0.83453 0.024 0.000 0.976 0.000 0.000 0.000
#> TCGA-06-0125-01A-01 3 0.0632 0.83453 0.024 0.000 0.976 0.000 0.000 0.000
#> TCGA-06-0126-01A-01 3 0.0632 0.83453 0.024 0.000 0.976 0.000 0.000 0.000
#> TCGA-06-0137-01A-03 3 0.0260 0.82564 0.000 0.000 0.992 0.000 0.008 0.000
#> TCGA-06-0145-01A-04 3 0.4047 0.43421 0.000 0.000 0.676 0.000 0.028 0.296
#> TCGA-06-0148-01A-01 3 0.3266 0.53511 0.000 0.000 0.728 0.000 0.272 0.000
#> TCGA-06-0187-01A-01 6 0.4923 0.22971 0.000 0.000 0.368 0.000 0.072 0.560
#> TCGA-06-0211-01B-01 3 0.3608 0.66357 0.196 0.000 0.776 0.008 0.012 0.008
#> TCGA-06-0402-01A-01 3 0.0790 0.83154 0.032 0.000 0.968 0.000 0.000 0.000
#> TCGA-08-0246-01A-01 2 0.1501 0.79018 0.000 0.924 0.000 0.000 0.000 0.076
#> TCGA-08-0354-01A-01 4 0.3759 0.72986 0.000 0.036 0.000 0.804 0.124 0.036
#> TCGA-08-0355-01A-01 5 0.4919 0.05299 0.000 0.004 0.008 0.424 0.528 0.036
#> TCGA-08-0357-01A-01 3 0.2733 0.77570 0.000 0.000 0.864 0.000 0.056 0.080
#> TCGA-08-0358-01A-01 5 0.3961 0.32317 0.000 0.000 0.016 0.276 0.700 0.008
#> TCGA-08-0375-01A-01 3 0.3917 0.61874 0.204 0.000 0.752 0.000 0.012 0.032
#> TCGA-08-0511-01A-01 3 0.1845 0.80694 0.000 0.000 0.920 0.000 0.028 0.052
#> TCGA-08-0514-01A-01 3 0.4269 0.43435 0.000 0.000 0.648 0.000 0.036 0.316
#> TCGA-08-0518-01A-01 3 0.0363 0.83115 0.012 0.000 0.988 0.000 0.000 0.000
#> TCGA-08-0529-01A-02 3 0.0993 0.82059 0.000 0.000 0.964 0.000 0.024 0.012
#> TCGA-08-0531-01A-01 3 0.2106 0.79856 0.000 0.000 0.904 0.000 0.032 0.064
#> TCGA-02-0057-01A-01 6 0.5170 0.40757 0.000 0.296 0.104 0.000 0.004 0.596
#> TCGA-02-0004-01A-01 2 0.0000 0.81637 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.3866 0.13001 0.000 0.516 0.000 0.000 0.000 0.484
#> TCGA-02-0025-01A-01 2 0.1492 0.79532 0.000 0.940 0.000 0.000 0.024 0.036
#> TCGA-02-0033-01A-01 2 0.2178 0.79067 0.000 0.868 0.000 0.000 0.000 0.132
#> TCGA-02-0034-01A-01 2 0.2178 0.79067 0.000 0.868 0.000 0.000 0.000 0.132
#> TCGA-02-0039-01A-01 2 0.1124 0.80313 0.000 0.956 0.000 0.000 0.008 0.036
#> TCGA-02-0051-01A-01 2 0.1124 0.80313 0.000 0.956 0.000 0.000 0.008 0.036
#> TCGA-02-0054-01A-01 2 0.3860 0.17701 0.000 0.528 0.000 0.000 0.000 0.472
#> TCGA-02-0055-01A-01 2 0.0146 0.81554 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-02-0059-01A-01 2 0.1225 0.80140 0.000 0.952 0.000 0.000 0.012 0.036
#> TCGA-02-0064-01A-01 2 0.3998 0.06591 0.000 0.504 0.000 0.000 0.004 0.492
#> TCGA-02-0075-01A-01 6 0.4661 -0.01147 0.000 0.464 0.032 0.000 0.004 0.500
#> TCGA-02-0079-01A-03 2 0.4709 0.23570 0.000 0.516 0.000 0.004 0.444 0.036
#> TCGA-02-0085-01A-01 2 0.1075 0.81646 0.000 0.952 0.000 0.000 0.000 0.048
#> TCGA-02-0086-01A-01 2 0.0000 0.81637 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0099-01A-01 6 0.4018 0.38876 0.000 0.324 0.000 0.000 0.020 0.656
#> TCGA-02-0106-01A-01 2 0.1501 0.80913 0.000 0.924 0.000 0.000 0.000 0.076
#> TCGA-02-0107-01A-01 2 0.0000 0.81637 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.1225 0.80140 0.000 0.952 0.000 0.000 0.012 0.036
#> TCGA-02-0326-01A-01 5 0.3678 0.37607 0.000 0.000 0.016 0.228 0.748 0.008
#> TCGA-02-0337-01A-01 2 0.4282 0.64071 0.000 0.720 0.000 0.000 0.192 0.088
#> TCGA-06-0122-01A-01 6 0.4625 0.19318 0.000 0.004 0.424 0.000 0.032 0.540
#> TCGA-06-0124-01A-01 2 0.4128 0.05225 0.000 0.500 0.004 0.000 0.004 0.492
#> TCGA-06-0130-01A-01 2 0.1957 0.80038 0.000 0.888 0.000 0.000 0.000 0.112
#> TCGA-06-0139-01A-01 2 0.0000 0.81637 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0143-01A-01 6 0.5038 0.28012 0.000 0.028 0.380 0.000 0.032 0.560
#> TCGA-06-0147-01A-01 2 0.1957 0.80038 0.000 0.888 0.000 0.000 0.000 0.112
#> TCGA-06-0149-01A-05 2 0.1408 0.79765 0.000 0.944 0.000 0.000 0.020 0.036
#> TCGA-06-0152-01A-02 5 0.4712 -0.00551 0.000 0.000 0.004 0.448 0.512 0.036
#> TCGA-06-0154-01A-02 2 0.2178 0.79067 0.000 0.868 0.000 0.000 0.000 0.132
#> TCGA-06-0164-01A-01 2 0.0632 0.81802 0.000 0.976 0.000 0.000 0.000 0.024
#> TCGA-06-0175-01A-01 6 0.3690 0.40142 0.000 0.308 0.008 0.000 0.000 0.684
#> TCGA-06-0176-01A-03 2 0.2178 0.79067 0.000 0.868 0.000 0.000 0.000 0.132
#> TCGA-06-0184-01A-01 2 0.0858 0.80808 0.000 0.968 0.000 0.004 0.000 0.028
#> TCGA-06-0189-01A-05 2 0.1225 0.80140 0.000 0.952 0.000 0.000 0.012 0.036
#> TCGA-06-0190-01A-01 2 0.2178 0.79067 0.000 0.868 0.000 0.000 0.000 0.132
#> TCGA-06-0194-01A-01 2 0.0000 0.81637 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0363 0.81394 0.000 0.988 0.000 0.000 0.000 0.012
#> TCGA-06-0210-01A-01 2 0.0146 0.81554 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-06-0397-01A-01 2 0.2219 0.78808 0.000 0.864 0.000 0.000 0.000 0.136
#> TCGA-06-0409-01A-02 2 0.1610 0.80918 0.000 0.916 0.000 0.000 0.000 0.084
#> TCGA-06-0412-01A-01 2 0.3390 0.58755 0.000 0.704 0.000 0.000 0.000 0.296
#> TCGA-06-0644-01A-02 2 0.0000 0.81637 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0937 0.81676 0.000 0.960 0.000 0.000 0.000 0.040
#> TCGA-08-0346-01A-01 2 0.1075 0.81725 0.000 0.952 0.000 0.000 0.000 0.048
#> TCGA-08-0352-01A-01 2 0.2278 0.79495 0.000 0.868 0.000 0.000 0.004 0.128
#> TCGA-08-0360-01A-01 2 0.1957 0.80038 0.000 0.888 0.000 0.000 0.000 0.112
#> TCGA-08-0390-01A-01 2 0.1930 0.78428 0.000 0.924 0.000 0.028 0.012 0.036
#> TCGA-08-0392-01A-01 2 0.4920 0.49971 0.000 0.692 0.000 0.204 0.068 0.036
#> TCGA-08-0509-01A-01 2 0.1814 0.80564 0.000 0.900 0.000 0.000 0.000 0.100
#> TCGA-08-0510-01A-01 6 0.3923 0.14589 0.000 0.416 0.000 0.000 0.004 0.580
#> TCGA-08-0512-01A-01 2 0.2178 0.79067 0.000 0.868 0.000 0.000 0.000 0.132
#> TCGA-08-0522-01A-01 2 0.2178 0.79067 0.000 0.868 0.000 0.000 0.000 0.132
#> TCGA-12-0619-01A-01 2 0.2178 0.79067 0.000 0.868 0.000 0.000 0.000 0.132
#> TCGA-12-0620-01A-01 2 0.3612 0.61443 0.000 0.764 0.000 0.000 0.200 0.036
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> ATC:skmeans 169 2.19e-25 2
#> ATC:skmeans 166 7.60e-35 3
#> ATC:skmeans 167 1.49e-67 4
#> ATC:skmeans 132 1.52e-64 5
#> ATC:skmeans 113 7.19e-60 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "pam"]
# you can also extract it by
# res = res_list["ATC:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.810 0.903 0.956 0.4100 0.568 0.568
#> 3 3 0.788 0.836 0.933 0.5726 0.780 0.613
#> 4 4 0.827 0.826 0.933 0.1289 0.852 0.614
#> 5 5 0.797 0.804 0.902 0.0616 0.925 0.739
#> 6 6 0.838 0.803 0.912 0.0409 0.959 0.826
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0047-01A-01 1 0.9775 0.4523 0.588 0.412
#> TCGA-02-0048-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.7299 0.7431 0.796 0.204
#> TCGA-02-0069-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.5059 0.8105 0.888 0.112
#> TCGA-02-0084-01A-03 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0087-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0104-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0321-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0325-01A-01 1 0.9732 0.3836 0.596 0.404
#> TCGA-02-0338-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0439-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0440-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.9710 0.4800 0.600 0.400
#> TCGA-06-0128-01A-01 1 0.9710 0.4800 0.600 0.400
#> TCGA-06-0129-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.9710 0.4800 0.600 0.400
#> TCGA-06-0166-01A-01 1 0.9710 0.4800 0.600 0.400
#> TCGA-06-0174-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-06-0238-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.0000 0.8788 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.9710 0.4800 0.600 0.400
#> TCGA-06-0413-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0648-01A-01 1 0.0376 0.8772 0.996 0.004
#> TCGA-08-0245-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-08-0347-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0348-01A-01 1 0.8713 0.6477 0.708 0.292
#> TCGA-08-0350-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0353-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.9710 0.4800 0.600 0.400
#> TCGA-08-0385-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-12-0616-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-12-0618-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0115-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0138-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.9129 0.5987 0.672 0.328
#> TCGA-06-0162-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.9710 0.4800 0.600 0.400
#> TCGA-06-0171-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0173-01A-01 2 0.9933 -0.0372 0.452 0.548
#> TCGA-06-0179-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0185-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.9710 0.4800 0.600 0.400
#> TCGA-06-0208-01B-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0221-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0237-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0240-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0349-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.8207 0.6906 0.744 0.256
#> TCGA-08-0520-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0007-01A-01 1 0.3431 0.8471 0.936 0.064
#> TCGA-02-0009-01A-01 1 0.0000 0.8788 1.000 0.000
#> TCGA-02-0016-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0021-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0023-01B-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.0672 0.8752 0.992 0.008
#> TCGA-02-0038-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0043-01A-01 1 0.7602 0.7076 0.780 0.220
#> TCGA-02-0070-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0102-01A-01 2 0.9710 0.2398 0.400 0.600
#> TCGA-02-0260-01A-03 2 0.9710 0.2398 0.400 0.600
#> TCGA-02-0269-01B-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0285-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0289-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0290-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0317-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0333-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0422-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0430-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0125-01A-01 1 0.7219 0.7303 0.800 0.200
#> TCGA-06-0126-01A-01 1 0.9358 0.5000 0.648 0.352
#> TCGA-06-0137-01A-03 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0145-01A-04 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0148-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0187-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0211-01B-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0402-01A-01 2 0.1414 0.9627 0.020 0.980
#> TCGA-08-0246-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0357-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0358-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0375-01A-01 2 0.7219 0.7013 0.200 0.800
#> TCGA-08-0511-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0514-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0518-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0529-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0531-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0057-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-02-0337-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0124-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9854 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9854 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.0000 0.9854 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 1 0.6168 0.42678 0.588 0.000 0.412
#> TCGA-02-0048-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.4605 0.72473 0.796 0.000 0.204
#> TCGA-02-0069-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.3192 0.79284 0.888 0.000 0.112
#> TCGA-02-0084-01A-03 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0087-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0104-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0325-01A-01 1 0.6140 0.34500 0.596 0.000 0.404
#> TCGA-02-0338-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0439-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0440-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.6126 0.45473 0.600 0.000 0.400
#> TCGA-06-0128-01A-01 1 0.6126 0.45473 0.600 0.000 0.400
#> TCGA-06-0129-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 1 0.6126 0.45473 0.600 0.000 0.400
#> TCGA-06-0166-01A-01 1 0.6126 0.45473 0.600 0.000 0.400
#> TCGA-06-0174-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-06-0238-01A-02 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-06-0410-01A-01 1 0.6126 0.45473 0.600 0.000 0.400
#> TCGA-06-0413-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0648-01A-01 1 0.0237 0.85982 0.996 0.000 0.004
#> TCGA-08-0245-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-08-0347-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0348-01A-01 1 0.5497 0.62443 0.708 0.000 0.292
#> TCGA-08-0350-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0353-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-08-0359-01A-01 1 0.6126 0.45473 0.600 0.000 0.400
#> TCGA-08-0385-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-12-0616-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-12-0618-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.0592 0.94625 0.000 0.988 0.012
#> TCGA-02-0113-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0115-01A-01 3 0.6168 0.30309 0.000 0.412 0.588
#> TCGA-02-0451-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0132-01A-02 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0133-01A-02 2 0.6026 0.36557 0.000 0.624 0.376
#> TCGA-06-0138-01A-02 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.5760 0.57406 0.672 0.000 0.328
#> TCGA-06-0162-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0167-01A-01 1 0.6126 0.45473 0.600 0.000 0.400
#> TCGA-06-0171-01A-02 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 3 0.6267 -0.00999 0.452 0.000 0.548
#> TCGA-06-0179-01A-02 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0182-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.6126 0.45473 0.600 0.000 0.400
#> TCGA-06-0208-01B-01 3 0.4235 0.76251 0.000 0.176 0.824
#> TCGA-06-0214-01A-02 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.6280 0.10609 0.000 0.540 0.460
#> TCGA-06-0221-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 3 0.3340 0.82613 0.000 0.120 0.880
#> TCGA-08-0349-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-08-0386-01A-01 1 0.5178 0.67071 0.744 0.000 0.256
#> TCGA-08-0520-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0007-01A-01 1 0.2165 0.83046 0.936 0.000 0.064
#> TCGA-02-0009-01A-01 1 0.0000 0.86147 1.000 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0021-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0023-01B-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.0424 0.85759 0.992 0.000 0.008
#> TCGA-02-0038-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0043-01A-01 1 0.4796 0.68570 0.780 0.000 0.220
#> TCGA-02-0070-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0102-01A-01 3 0.6126 0.26056 0.400 0.000 0.600
#> TCGA-02-0260-01A-03 3 0.6126 0.26056 0.400 0.000 0.600
#> TCGA-02-0269-01B-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0285-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0289-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0290-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0317-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0333-01A-02 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0422-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0430-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0125-01A-01 1 0.4555 0.71008 0.800 0.000 0.200
#> TCGA-06-0126-01A-01 1 0.5905 0.46586 0.648 0.000 0.352
#> TCGA-06-0137-01A-03 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0145-01A-04 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0148-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0187-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0211-01B-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0402-01A-01 3 0.0892 0.91778 0.020 0.000 0.980
#> TCGA-08-0246-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0354-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0355-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0357-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0358-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0375-01A-01 3 0.4555 0.68589 0.200 0.000 0.800
#> TCGA-08-0511-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0514-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0518-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0529-01A-02 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0531-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0057-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 3 0.2711 0.85550 0.000 0.088 0.912
#> TCGA-02-0039-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-02-0054-01A-01 3 0.4291 0.75746 0.000 0.180 0.820
#> TCGA-02-0055-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-02-0064-01A-01 2 0.1643 0.91296 0.000 0.956 0.044
#> TCGA-02-0075-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0079-01A-03 3 0.4555 0.71884 0.000 0.200 0.800
#> TCGA-02-0085-01A-01 2 0.5926 0.43439 0.000 0.644 0.356
#> TCGA-02-0086-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-02-0099-01A-01 3 0.4654 0.71817 0.000 0.208 0.792
#> TCGA-02-0106-01A-01 3 0.6299 0.10882 0.000 0.476 0.524
#> TCGA-02-0107-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-02-0326-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-02-0337-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0122-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0124-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0143-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0147-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0152-01A-02 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0154-01A-02 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-06-0176-01A-03 3 0.5760 0.50836 0.000 0.328 0.672
#> TCGA-06-0184-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0210-01A-01 2 0.5058 0.64984 0.000 0.756 0.244
#> TCGA-06-0397-01A-01 2 0.0592 0.94609 0.000 0.988 0.012
#> TCGA-06-0409-01A-02 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0412-01A-01 3 0.0237 0.93315 0.000 0.004 0.996
#> TCGA-06-0644-01A-02 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-08-0352-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-08-0392-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.95710 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 3 0.0000 0.93637 0.000 0.000 1.000
#> TCGA-12-0620-01A-01 3 0.6095 0.32503 0.000 0.392 0.608
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 4 0.5620 0.24386 0.416 0.000 0.024 0.560
#> TCGA-02-0048-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.4730 0.40538 0.636 0.000 0.364 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.2530 0.81020 0.888 0.000 0.112 0.000
#> TCGA-02-0084-01A-03 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0087-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0104-01A-01 4 0.4999 0.04471 0.492 0.000 0.000 0.508
#> TCGA-02-0114-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0325-01A-01 3 0.5000 -0.05346 0.496 0.000 0.504 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0432-01A-02 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0439-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 3 0.4898 0.26439 0.416 0.000 0.584 0.000
#> TCGA-06-0128-01A-01 4 0.3606 0.80268 0.024 0.000 0.132 0.844
#> TCGA-06-0129-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-06-0156-01A-01 3 0.7251 -0.00908 0.416 0.000 0.440 0.144
#> TCGA-06-0166-01A-01 3 0.4898 0.26439 0.416 0.000 0.584 0.000
#> TCGA-06-0174-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.1867 0.84891 0.928 0.000 0.072 0.000
#> TCGA-06-0238-01A-02 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0413-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0648-01A-01 1 0.3486 0.72882 0.812 0.000 0.188 0.000
#> TCGA-08-0245-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-08-0348-01A-01 1 0.4992 0.06246 0.524 0.000 0.476 0.000
#> TCGA-08-0350-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-08-0353-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-08-0359-01A-01 3 0.4898 0.26439 0.416 0.000 0.584 0.000
#> TCGA-08-0385-01A-01 1 0.3444 0.73328 0.816 0.000 0.184 0.000
#> TCGA-08-0517-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 4 0.3486 0.75170 0.000 0.000 0.188 0.812
#> TCGA-12-0618-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.4790 0.38715 0.000 0.620 0.000 0.380
#> TCGA-02-0113-01A-01 4 0.4431 0.54473 0.000 0.000 0.304 0.696
#> TCGA-02-0115-01A-01 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.0336 0.96022 0.000 0.992 0.000 0.008
#> TCGA-06-0132-01A-02 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0133-01A-02 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 4 0.2408 0.82453 0.104 0.000 0.000 0.896
#> TCGA-06-0162-01A-01 4 0.3528 0.71340 0.000 0.192 0.000 0.808
#> TCGA-06-0167-01A-01 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0171-01A-02 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 3 0.5807 0.34025 0.364 0.000 0.596 0.040
#> TCGA-06-0179-01A-02 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 4 0.3764 0.71405 0.000 0.000 0.216 0.784
#> TCGA-06-0195-01B-01 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0208-01B-01 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0219-01A-01 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-08-0349-01A-01 4 0.0000 0.90587 0.000 0.000 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-08-0386-01A-01 1 0.4103 0.62399 0.744 0.000 0.256 0.000
#> TCGA-08-0520-01A-01 4 0.1118 0.88491 0.000 0.000 0.036 0.964
#> TCGA-02-0007-01A-01 1 0.1637 0.86346 0.940 0.000 0.060 0.000
#> TCGA-02-0009-01A-01 1 0.0000 0.90618 1.000 0.000 0.000 0.000
#> TCGA-02-0016-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0021-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0023-01B-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0027-01A-01 1 0.0336 0.90073 0.992 0.000 0.008 0.000
#> TCGA-02-0038-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0043-01A-01 1 0.3801 0.68838 0.780 0.000 0.220 0.000
#> TCGA-02-0070-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0102-01A-01 1 0.4898 0.28894 0.584 0.000 0.416 0.000
#> TCGA-02-0260-01A-03 3 0.4855 0.26707 0.400 0.000 0.600 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0125-01A-01 1 0.3610 0.71280 0.800 0.000 0.200 0.000
#> TCGA-06-0126-01A-01 1 0.4661 0.46116 0.652 0.000 0.348 0.000
#> TCGA-06-0137-01A-03 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0145-01A-04 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0402-01A-01 3 0.1118 0.87246 0.036 0.000 0.964 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-08-0354-01A-01 3 0.4713 0.41480 0.000 0.000 0.640 0.360
#> TCGA-08-0355-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-08-0357-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-08-0358-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-08-0375-01A-01 3 0.3610 0.68402 0.200 0.000 0.800 0.000
#> TCGA-08-0511-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-08-0518-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-08-0529-01A-02 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0057-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0004-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 3 0.2149 0.82545 0.000 0.088 0.912 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-02-0054-01A-01 3 0.3400 0.73156 0.000 0.180 0.820 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.1302 0.91650 0.000 0.956 0.044 0.000
#> TCGA-02-0075-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0079-01A-03 3 0.3610 0.70777 0.000 0.200 0.800 0.000
#> TCGA-02-0085-01A-01 2 0.4697 0.41750 0.000 0.644 0.356 0.000
#> TCGA-02-0086-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-02-0099-01A-01 3 0.3688 0.69942 0.000 0.208 0.792 0.000
#> TCGA-02-0106-01A-01 3 0.4992 0.13410 0.000 0.476 0.524 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-02-0337-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0122-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0124-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0154-01A-02 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-06-0176-01A-03 3 0.4564 0.50646 0.000 0.328 0.672 0.000
#> TCGA-06-0184-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.4008 0.64167 0.000 0.756 0.244 0.000
#> TCGA-06-0397-01A-01 2 0.0469 0.95429 0.000 0.988 0.012 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 3 0.0188 0.89622 0.000 0.004 0.996 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-08-0352-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-08-0392-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.96709 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 3 0.0000 0.89915 0.000 0.000 1.000 0.000
#> TCGA-12-0620-01A-01 3 0.4830 0.35370 0.000 0.392 0.608 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.1121 0.796 0.956 0.000 0.000 0.000 0.044
#> TCGA-02-0010-01A-01 5 0.3636 0.808 0.272 0.000 0.000 0.000 0.728
#> TCGA-02-0011-01B-01 1 0.1410 0.791 0.940 0.000 0.000 0.000 0.060
#> TCGA-02-0014-01A-01 5 0.3636 0.808 0.272 0.000 0.000 0.000 0.728
#> TCGA-02-0024-01B-01 5 0.3636 0.808 0.272 0.000 0.000 0.000 0.728
#> TCGA-02-0026-01B-01 5 0.3636 0.808 0.272 0.000 0.000 0.000 0.728
#> TCGA-02-0028-01A-01 5 0.3636 0.808 0.272 0.000 0.000 0.000 0.728
#> TCGA-02-0046-01A-01 1 0.1544 0.786 0.932 0.000 0.000 0.000 0.068
#> TCGA-02-0047-01A-01 1 0.4321 0.350 0.600 0.000 0.004 0.396 0.000
#> TCGA-02-0048-01A-01 1 0.1121 0.796 0.956 0.000 0.000 0.000 0.044
#> TCGA-02-0060-01A-01 1 0.1410 0.793 0.940 0.000 0.000 0.000 0.060
#> TCGA-02-0069-01A-01 5 0.3636 0.808 0.272 0.000 0.000 0.000 0.728
#> TCGA-02-0074-01A-01 1 0.1965 0.766 0.904 0.000 0.000 0.000 0.096
#> TCGA-02-0080-01A-01 5 0.0000 0.688 0.000 0.000 0.000 0.000 1.000
#> TCGA-02-0084-01A-03 3 0.0162 0.892 0.004 0.000 0.996 0.000 0.000
#> TCGA-02-0087-01A-01 3 0.1121 0.872 0.044 0.000 0.956 0.000 0.000
#> TCGA-02-0104-01A-01 1 0.5744 0.391 0.564 0.000 0.000 0.332 0.104
#> TCGA-02-0114-01A-01 1 0.3796 0.411 0.700 0.000 0.000 0.000 0.300
#> TCGA-02-0281-01A-01 5 0.3636 0.808 0.272 0.000 0.000 0.000 0.728
#> TCGA-02-0321-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0325-01A-01 5 0.2690 0.603 0.156 0.000 0.000 0.000 0.844
#> TCGA-02-0338-01A-01 5 0.3636 0.808 0.272 0.000 0.000 0.000 0.728
#> TCGA-02-0339-01A-01 5 0.3561 0.799 0.260 0.000 0.000 0.000 0.740
#> TCGA-02-0432-01A-02 1 0.2605 0.779 0.852 0.000 0.000 0.000 0.148
#> TCGA-02-0439-01A-01 3 0.3390 0.788 0.100 0.000 0.840 0.000 0.060
#> TCGA-02-0440-01A-01 1 0.0000 0.801 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.2127 0.746 0.892 0.000 0.108 0.000 0.000
#> TCGA-06-0128-01A-01 4 0.4752 0.506 0.316 0.000 0.036 0.648 0.000
#> TCGA-06-0129-01A-01 5 0.1671 0.709 0.076 0.000 0.000 0.000 0.924
#> TCGA-06-0146-01A-01 5 0.1478 0.709 0.064 0.000 0.000 0.000 0.936
#> TCGA-06-0156-01A-01 1 0.2127 0.746 0.892 0.000 0.108 0.000 0.000
#> TCGA-06-0166-01A-01 1 0.3074 0.625 0.804 0.000 0.196 0.000 0.000
#> TCGA-06-0174-01A-01 1 0.1121 0.796 0.956 0.000 0.000 0.000 0.044
#> TCGA-06-0177-01A-01 1 0.1410 0.793 0.940 0.000 0.000 0.000 0.060
#> TCGA-06-0238-01A-02 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.801 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0413-01A-01 5 0.3636 0.808 0.272 0.000 0.000 0.000 0.728
#> TCGA-06-0414-01A-01 1 0.0963 0.799 0.964 0.000 0.000 0.000 0.036
#> TCGA-06-0646-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0648-01A-01 1 0.1410 0.793 0.940 0.000 0.000 0.000 0.060
#> TCGA-08-0245-01A-01 1 0.1121 0.796 0.956 0.000 0.000 0.000 0.044
#> TCGA-08-0344-01A-01 1 0.4161 0.342 0.608 0.000 0.000 0.000 0.392
#> TCGA-08-0347-01A-01 3 0.1121 0.872 0.044 0.000 0.956 0.000 0.000
#> TCGA-08-0348-01A-01 1 0.1410 0.793 0.940 0.000 0.000 0.000 0.060
#> TCGA-08-0350-01A-01 3 0.5086 0.499 0.304 0.000 0.636 0.000 0.060
#> TCGA-08-0353-01A-01 1 0.0000 0.801 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0359-01A-01 1 0.2127 0.746 0.892 0.000 0.108 0.000 0.000
#> TCGA-08-0385-01A-01 1 0.1410 0.793 0.940 0.000 0.000 0.000 0.060
#> TCGA-08-0517-01A-01 1 0.1121 0.796 0.956 0.000 0.000 0.000 0.044
#> TCGA-08-0524-01A-01 5 0.3636 0.808 0.272 0.000 0.000 0.000 0.728
#> TCGA-12-0616-01A-01 4 0.3003 0.719 0.000 0.000 0.188 0.812 0.000
#> TCGA-12-0618-01A-01 1 0.2516 0.784 0.860 0.000 0.000 0.000 0.140
#> TCGA-02-0089-01A-01 2 0.4126 0.390 0.000 0.620 0.000 0.380 0.000
#> TCGA-02-0113-01A-01 4 0.3816 0.543 0.000 0.000 0.304 0.696 0.000
#> TCGA-02-0115-01A-01 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0451-01A-01 2 0.0290 0.960 0.000 0.992 0.000 0.008 0.000
#> TCGA-06-0132-01A-02 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0133-01A-02 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0138-01A-02 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0160-01A-01 4 0.5218 0.420 0.336 0.000 0.000 0.604 0.060
#> TCGA-06-0162-01A-01 4 0.3039 0.703 0.000 0.192 0.000 0.808 0.000
#> TCGA-06-0167-01A-01 4 0.2514 0.838 0.044 0.000 0.000 0.896 0.060
#> TCGA-06-0171-01A-02 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0173-01A-01 3 0.5059 0.172 0.416 0.000 0.548 0.036 0.000
#> TCGA-06-0179-01A-02 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0182-01A-01 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0185-01A-01 4 0.3242 0.684 0.000 0.000 0.216 0.784 0.000
#> TCGA-06-0195-01B-01 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0208-01B-01 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0214-01A-02 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0219-01A-01 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0221-01A-01 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0237-01A-02 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0240-01A-02 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-08-0349-01A-01 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000
#> TCGA-08-0380-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0386-01A-01 1 0.2732 0.668 0.840 0.000 0.160 0.000 0.000
#> TCGA-08-0520-01A-01 4 0.0963 0.876 0.000 0.000 0.036 0.964 0.000
#> TCGA-02-0007-01A-01 1 0.3595 0.679 0.816 0.000 0.140 0.000 0.044
#> TCGA-02-0009-01A-01 1 0.3534 0.584 0.744 0.000 0.000 0.000 0.256
#> TCGA-02-0016-01A-01 3 0.3696 0.740 0.016 0.000 0.772 0.000 0.212
#> TCGA-02-0021-01A-01 3 0.4264 0.717 0.044 0.000 0.744 0.000 0.212
#> TCGA-02-0023-01B-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0027-01A-01 1 0.3210 0.597 0.788 0.000 0.000 0.000 0.212
#> TCGA-02-0038-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0043-01A-01 5 0.4030 0.414 0.352 0.000 0.000 0.000 0.648
#> TCGA-02-0070-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0102-01A-01 3 0.6477 0.304 0.248 0.000 0.496 0.000 0.256
#> TCGA-02-0260-01A-03 5 0.3487 0.470 0.008 0.000 0.212 0.000 0.780
#> TCGA-02-0269-01B-01 3 0.2104 0.849 0.024 0.000 0.916 0.000 0.060
#> TCGA-02-0285-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0289-01A-01 3 0.0963 0.876 0.036 0.000 0.964 0.000 0.000
#> TCGA-02-0290-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0333-01A-02 3 0.0290 0.890 0.008 0.000 0.992 0.000 0.000
#> TCGA-02-0422-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0430-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0125-01A-01 5 0.3480 0.590 0.248 0.000 0.000 0.000 0.752
#> TCGA-06-0126-01A-01 1 0.5806 0.363 0.600 0.000 0.144 0.000 0.256
#> TCGA-06-0137-01A-03 3 0.4193 0.720 0.040 0.000 0.748 0.000 0.212
#> TCGA-06-0145-01A-04 3 0.3210 0.751 0.000 0.000 0.788 0.000 0.212
#> TCGA-06-0148-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0187-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0211-01B-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0402-01A-01 3 0.1478 0.862 0.064 0.000 0.936 0.000 0.000
#> TCGA-08-0246-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0354-01A-01 3 0.4060 0.452 0.000 0.000 0.640 0.360 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0357-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0358-01A-01 3 0.0963 0.876 0.000 0.000 0.964 0.000 0.036
#> TCGA-08-0375-01A-01 3 0.4269 0.641 0.232 0.000 0.732 0.000 0.036
#> TCGA-08-0511-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0514-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0518-01A-01 3 0.2920 0.810 0.016 0.000 0.852 0.000 0.132
#> TCGA-08-0529-01A-02 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0057-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0004-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0025-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 3 0.1851 0.836 0.000 0.088 0.912 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0054-01A-01 3 0.2929 0.753 0.000 0.180 0.820 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.1121 0.917 0.000 0.956 0.044 0.000 0.000
#> TCGA-02-0075-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0079-01A-03 3 0.3109 0.720 0.000 0.200 0.800 0.000 0.000
#> TCGA-02-0085-01A-01 2 0.4045 0.411 0.000 0.644 0.356 0.000 0.000
#> TCGA-02-0086-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0099-01A-01 3 0.3177 0.723 0.000 0.208 0.792 0.000 0.000
#> TCGA-02-0106-01A-01 3 0.4300 0.186 0.000 0.476 0.524 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0337-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0122-01A-01 3 0.3210 0.751 0.000 0.000 0.788 0.000 0.212
#> TCGA-06-0124-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.3210 0.751 0.000 0.000 0.788 0.000 0.212
#> TCGA-06-0147-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0154-01A-02 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0176-01A-03 3 0.3932 0.542 0.000 0.328 0.672 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.3452 0.636 0.000 0.756 0.244 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0404 0.954 0.000 0.988 0.012 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0412-01A-01 3 0.0162 0.891 0.000 0.004 0.996 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0352-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0392-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 3 0.0000 0.893 0.000 0.000 1.000 0.000 0.000
#> TCGA-12-0620-01A-01 3 0.4161 0.384 0.000 0.392 0.608 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.1141 0.838 0.948 0.000 0.000 0.000 0.000 0.052
#> TCGA-02-0010-01A-01 5 0.0000 0.961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.1391 0.839 0.944 0.000 0.000 0.000 0.016 0.040
#> TCGA-02-0014-01A-01 5 0.0000 0.961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0024-01B-01 5 0.0000 0.961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0026-01B-01 5 0.0000 0.961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0028-01A-01 5 0.0000 0.961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.2066 0.825 0.908 0.000 0.000 0.000 0.052 0.040
#> TCGA-02-0047-01A-01 1 0.3742 0.485 0.648 0.000 0.004 0.348 0.000 0.000
#> TCGA-02-0048-01A-01 1 0.1814 0.819 0.900 0.000 0.000 0.000 0.000 0.100
#> TCGA-02-0060-01A-01 1 0.2558 0.758 0.840 0.000 0.004 0.000 0.000 0.156
#> TCGA-02-0069-01A-01 5 0.0000 0.961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.4482 0.500 0.600 0.000 0.000 0.000 0.360 0.040
#> TCGA-02-0080-01A-01 5 0.3841 0.381 0.004 0.000 0.000 0.000 0.616 0.380
#> TCGA-02-0084-01A-03 3 0.0146 0.865 0.004 0.000 0.996 0.000 0.000 0.000
#> TCGA-02-0087-01A-01 3 0.1714 0.810 0.092 0.000 0.908 0.000 0.000 0.000
#> TCGA-02-0104-01A-01 1 0.5133 0.383 0.592 0.000 0.000 0.332 0.024 0.052
#> TCGA-02-0114-01A-01 1 0.3490 0.739 0.784 0.000 0.000 0.000 0.176 0.040
#> TCGA-02-0281-01A-01 5 0.0000 0.961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0321-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0325-01A-01 6 0.3295 0.646 0.056 0.000 0.000 0.000 0.128 0.816
#> TCGA-02-0338-01A-01 5 0.0000 0.961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0339-01A-01 5 0.0000 0.961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.3319 0.770 0.800 0.000 0.000 0.000 0.164 0.036
#> TCGA-02-0439-01A-01 3 0.2219 0.772 0.136 0.000 0.864 0.000 0.000 0.000
#> TCGA-02-0440-01A-01 1 0.0000 0.837 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-02-0446-01A-01 1 0.3167 0.753 0.832 0.000 0.096 0.000 0.000 0.072
#> TCGA-06-0128-01A-01 4 0.4373 0.603 0.260 0.000 0.008 0.688 0.000 0.044
#> TCGA-06-0129-01A-01 5 0.1152 0.921 0.004 0.000 0.000 0.000 0.952 0.044
#> TCGA-06-0146-01A-01 5 0.0865 0.930 0.000 0.000 0.000 0.000 0.964 0.036
#> TCGA-06-0156-01A-01 1 0.2768 0.757 0.832 0.000 0.012 0.000 0.000 0.156
#> TCGA-06-0166-01A-01 1 0.3073 0.657 0.788 0.000 0.204 0.000 0.000 0.008
#> TCGA-06-0174-01A-01 1 0.1141 0.838 0.948 0.000 0.000 0.000 0.000 0.052
#> TCGA-06-0177-01A-01 1 0.0632 0.836 0.976 0.000 0.000 0.000 0.000 0.024
#> TCGA-06-0238-01A-02 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0241-01A-02 1 0.0000 0.837 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-06-0410-01A-01 4 0.2092 0.809 0.124 0.000 0.000 0.876 0.000 0.000
#> TCGA-06-0413-01A-01 5 0.0000 0.961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.0937 0.840 0.960 0.000 0.000 0.000 0.000 0.040
#> TCGA-06-0646-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0648-01A-01 1 0.0000 0.837 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-08-0245-01A-01 1 0.1204 0.837 0.944 0.000 0.000 0.000 0.000 0.056
#> TCGA-08-0344-01A-01 1 0.3101 0.681 0.756 0.000 0.000 0.000 0.244 0.000
#> TCGA-08-0347-01A-01 3 0.1714 0.810 0.092 0.000 0.908 0.000 0.000 0.000
#> TCGA-08-0348-01A-01 1 0.0937 0.833 0.960 0.000 0.000 0.000 0.000 0.040
#> TCGA-08-0350-01A-01 3 0.3023 0.659 0.232 0.000 0.768 0.000 0.000 0.000
#> TCGA-08-0353-01A-01 1 0.2854 0.720 0.792 0.000 0.000 0.000 0.000 0.208
#> TCGA-08-0359-01A-01 1 0.2527 0.704 0.832 0.000 0.168 0.000 0.000 0.000
#> TCGA-08-0385-01A-01 1 0.0000 0.837 1.000 0.000 0.000 0.000 0.000 0.000
#> TCGA-08-0517-01A-01 1 0.1765 0.830 0.904 0.000 0.000 0.000 0.000 0.096
#> TCGA-08-0524-01A-01 5 0.0000 0.961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-12-0616-01A-01 4 0.2697 0.717 0.000 0.000 0.188 0.812 0.000 0.000
#> TCGA-12-0618-01A-01 1 0.2129 0.824 0.904 0.000 0.000 0.000 0.056 0.040
#> TCGA-02-0089-01A-01 2 0.3706 0.395 0.000 0.620 0.000 0.380 0.000 0.000
#> TCGA-02-0113-01A-01 4 0.3428 0.521 0.000 0.000 0.304 0.696 0.000 0.000
#> TCGA-02-0115-01A-01 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-02-0451-01A-01 2 0.0260 0.959 0.000 0.992 0.000 0.008 0.000 0.000
#> TCGA-06-0132-01A-02 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0133-01A-02 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0138-01A-02 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0160-01A-01 4 0.3984 0.516 0.336 0.000 0.000 0.648 0.000 0.016
#> TCGA-06-0162-01A-01 4 0.2730 0.700 0.000 0.192 0.000 0.808 0.000 0.000
#> TCGA-06-0167-01A-01 4 0.1908 0.838 0.096 0.000 0.000 0.900 0.000 0.004
#> TCGA-06-0171-01A-02 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0173-01A-01 3 0.4771 0.130 0.412 0.000 0.544 0.036 0.000 0.008
#> TCGA-06-0179-01A-02 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0182-01A-01 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0185-01A-01 4 0.2912 0.680 0.000 0.000 0.216 0.784 0.000 0.000
#> TCGA-06-0195-01B-01 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0208-01B-01 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0214-01A-02 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0219-01A-01 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0221-01A-01 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0237-01A-02 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0240-01A-02 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0349-01A-01 4 0.0000 0.902 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0380-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0386-01A-01 1 0.4522 0.592 0.672 0.000 0.076 0.000 0.000 0.252
#> TCGA-08-0520-01A-01 4 0.0865 0.877 0.000 0.000 0.036 0.964 0.000 0.000
#> TCGA-02-0007-01A-01 6 0.4552 0.148 0.364 0.000 0.044 0.000 0.000 0.592
#> TCGA-02-0009-01A-01 6 0.0363 0.780 0.012 0.000 0.000 0.000 0.000 0.988
#> TCGA-02-0016-01A-01 6 0.2378 0.716 0.000 0.000 0.152 0.000 0.000 0.848
#> TCGA-02-0021-01A-01 6 0.1462 0.774 0.008 0.000 0.056 0.000 0.000 0.936
#> TCGA-02-0023-01B-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0027-01A-01 6 0.2730 0.678 0.192 0.000 0.000 0.000 0.000 0.808
#> TCGA-02-0038-01A-01 3 0.0458 0.860 0.000 0.000 0.984 0.000 0.000 0.016
#> TCGA-02-0043-01A-01 6 0.0632 0.780 0.024 0.000 0.000 0.000 0.000 0.976
#> TCGA-02-0070-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0102-01A-01 6 0.0547 0.780 0.020 0.000 0.000 0.000 0.000 0.980
#> TCGA-02-0260-01A-03 6 0.2527 0.647 0.000 0.000 0.000 0.000 0.168 0.832
#> TCGA-02-0269-01B-01 3 0.3309 0.580 0.000 0.000 0.720 0.000 0.000 0.280
#> TCGA-02-0285-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0289-01A-01 3 0.1152 0.847 0.004 0.000 0.952 0.000 0.000 0.044
#> TCGA-02-0290-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0317-01A-01 3 0.0458 0.861 0.000 0.000 0.984 0.000 0.000 0.016
#> TCGA-02-0333-01A-02 3 0.0632 0.859 0.000 0.000 0.976 0.000 0.000 0.024
#> TCGA-02-0422-01A-01 3 0.1327 0.831 0.000 0.000 0.936 0.000 0.000 0.064
#> TCGA-02-0430-01A-01 3 0.2969 0.654 0.000 0.000 0.776 0.000 0.000 0.224
#> TCGA-06-0125-01A-01 6 0.0260 0.779 0.008 0.000 0.000 0.000 0.000 0.992
#> TCGA-06-0126-01A-01 6 0.0632 0.780 0.024 0.000 0.000 0.000 0.000 0.976
#> TCGA-06-0137-01A-03 6 0.1196 0.776 0.008 0.000 0.040 0.000 0.000 0.952
#> TCGA-06-0145-01A-04 6 0.3782 0.269 0.000 0.000 0.412 0.000 0.000 0.588
#> TCGA-06-0148-01A-01 3 0.0458 0.861 0.000 0.000 0.984 0.000 0.000 0.016
#> TCGA-06-0187-01A-01 3 0.1267 0.834 0.000 0.000 0.940 0.000 0.000 0.060
#> TCGA-06-0211-01B-01 3 0.2969 0.654 0.000 0.000 0.776 0.000 0.000 0.224
#> TCGA-06-0402-01A-01 6 0.4388 0.305 0.028 0.000 0.400 0.000 0.000 0.572
#> TCGA-08-0246-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0354-01A-01 3 0.3647 0.468 0.000 0.000 0.640 0.360 0.000 0.000
#> TCGA-08-0355-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0357-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0358-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0375-01A-01 3 0.4668 0.413 0.064 0.000 0.620 0.000 0.000 0.316
#> TCGA-08-0511-01A-01 3 0.1957 0.788 0.000 0.000 0.888 0.000 0.000 0.112
#> TCGA-08-0514-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0518-01A-01 6 0.2703 0.706 0.004 0.000 0.172 0.000 0.000 0.824
#> TCGA-08-0529-01A-02 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0531-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0057-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0004-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.0260 0.961 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-02-0025-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0034-01A-01 3 0.1866 0.806 0.000 0.084 0.908 0.000 0.000 0.008
#> TCGA-02-0039-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0054-01A-01 3 0.2882 0.693 0.000 0.180 0.812 0.000 0.000 0.008
#> TCGA-02-0055-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.1265 0.912 0.000 0.948 0.044 0.000 0.000 0.008
#> TCGA-02-0075-01A-01 3 0.0363 0.864 0.000 0.000 0.988 0.000 0.000 0.012
#> TCGA-02-0079-01A-03 3 0.2793 0.682 0.000 0.200 0.800 0.000 0.000 0.000
#> TCGA-02-0085-01A-01 2 0.3874 0.382 0.000 0.636 0.356 0.000 0.000 0.008
#> TCGA-02-0086-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0099-01A-01 3 0.3290 0.650 0.000 0.208 0.776 0.000 0.000 0.016
#> TCGA-02-0106-01A-01 3 0.4089 0.186 0.000 0.468 0.524 0.000 0.000 0.008
#> TCGA-02-0107-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-02-0337-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0122-01A-01 3 0.3765 0.240 0.000 0.000 0.596 0.000 0.000 0.404
#> TCGA-06-0124-01A-01 3 0.0260 0.864 0.000 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0130-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.3659 0.346 0.000 0.000 0.636 0.000 0.000 0.364
#> TCGA-06-0147-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0149-01A-05 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0152-01A-02 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0154-01A-02 3 0.0260 0.864 0.000 0.000 0.992 0.000 0.000 0.008
#> TCGA-06-0164-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0176-01A-03 3 0.3774 0.473 0.000 0.328 0.664 0.000 0.000 0.008
#> TCGA-06-0184-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0260 0.961 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-06-0194-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.3298 0.634 0.000 0.756 0.236 0.000 0.000 0.008
#> TCGA-06-0397-01A-01 2 0.0622 0.950 0.000 0.980 0.012 0.000 0.000 0.008
#> TCGA-06-0409-01A-02 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0412-01A-01 3 0.0405 0.863 0.000 0.004 0.988 0.000 0.000 0.008
#> TCGA-06-0644-01A-02 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0352-01A-01 3 0.0000 0.866 0.000 0.000 1.000 0.000 0.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0392-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0509-01A-01 2 0.0000 0.965 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0510-01A-01 2 0.0260 0.961 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-08-0512-01A-01 2 0.0260 0.961 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-08-0522-01A-01 2 0.0260 0.961 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-12-0619-01A-01 3 0.0260 0.864 0.000 0.000 0.992 0.000 0.000 0.008
#> TCGA-12-0620-01A-01 3 0.3737 0.399 0.000 0.392 0.608 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> ATC:pam 159 1.03e-19 2
#> ATC:pam 153 2.03e-26 3
#> ATC:pam 155 6.43e-47 4
#> ATC:pam 157 1.29e-47 5
#> ATC:pam 156 1.36e-52 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "mclust"]
# you can also extract it by
# res = res_list["ATC:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.462 0.857 0.903 0.4164 0.602 0.602
#> 3 3 0.445 0.623 0.810 0.4865 0.602 0.413
#> 4 4 0.733 0.835 0.925 0.0697 0.785 0.528
#> 5 5 0.607 0.580 0.793 0.1448 0.813 0.495
#> 6 6 0.659 0.679 0.794 0.0625 0.837 0.412
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.1633 0.8774 0.976 0.024
#> TCGA-02-0010-01A-01 1 0.6247 0.8629 0.844 0.156
#> TCGA-02-0011-01B-01 1 0.5737 0.8696 0.864 0.136
#> TCGA-02-0014-01A-01 1 0.6247 0.8629 0.844 0.156
#> TCGA-02-0024-01B-01 1 0.5842 0.8684 0.860 0.140
#> TCGA-02-0026-01B-01 1 0.5737 0.8696 0.864 0.136
#> TCGA-02-0028-01A-01 1 0.6247 0.8629 0.844 0.156
#> TCGA-02-0046-01A-01 1 0.6247 0.8629 0.844 0.156
#> TCGA-02-0047-01A-01 1 0.6343 0.8629 0.840 0.160
#> TCGA-02-0048-01A-01 1 0.6247 0.8629 0.844 0.156
#> TCGA-02-0060-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-02-0069-01A-01 1 0.6247 0.8629 0.844 0.156
#> TCGA-02-0074-01A-01 1 0.6247 0.8629 0.844 0.156
#> TCGA-02-0080-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-02-0084-01A-03 1 0.5519 0.8438 0.872 0.128
#> TCGA-02-0087-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-02-0104-01A-01 1 0.0000 0.8760 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.1633 0.8774 0.976 0.024
#> TCGA-02-0281-01A-01 1 0.5737 0.8696 0.864 0.136
#> TCGA-02-0321-01A-01 1 0.3431 0.8785 0.936 0.064
#> TCGA-02-0325-01A-01 1 0.3274 0.8791 0.940 0.060
#> TCGA-02-0338-01A-01 1 0.5842 0.8684 0.860 0.140
#> TCGA-02-0339-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-02-0432-01A-02 1 0.0376 0.8778 0.996 0.004
#> TCGA-02-0439-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-02-0440-01A-01 1 0.6247 0.8629 0.844 0.156
#> TCGA-02-0446-01A-01 1 0.6973 0.8468 0.812 0.188
#> TCGA-06-0128-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-06-0129-01A-01 1 0.6247 0.8629 0.844 0.156
#> TCGA-06-0146-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-06-0156-01A-01 1 0.6343 0.8629 0.840 0.160
#> TCGA-06-0166-01A-01 1 0.6343 0.8629 0.840 0.160
#> TCGA-06-0174-01A-01 1 0.1633 0.8774 0.976 0.024
#> TCGA-06-0177-01A-01 1 0.2603 0.8844 0.956 0.044
#> TCGA-06-0238-01A-02 1 0.0376 0.8770 0.996 0.004
#> TCGA-06-0241-01A-02 1 0.1633 0.8774 0.976 0.024
#> TCGA-06-0410-01A-01 1 0.0000 0.8760 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.5842 0.8684 0.860 0.140
#> TCGA-06-0414-01A-01 1 0.1633 0.8774 0.976 0.024
#> TCGA-06-0646-01A-01 1 0.5946 0.8683 0.856 0.144
#> TCGA-06-0648-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-08-0245-01A-01 1 0.4690 0.8795 0.900 0.100
#> TCGA-08-0344-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-08-0347-01A-01 1 0.7139 0.8520 0.804 0.196
#> TCGA-08-0348-01A-01 1 0.5737 0.8696 0.864 0.136
#> TCGA-08-0350-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-08-0353-01A-01 1 0.6801 0.8587 0.820 0.180
#> TCGA-08-0359-01A-01 1 0.2778 0.8845 0.952 0.048
#> TCGA-08-0385-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-08-0517-01A-01 1 0.6247 0.8629 0.844 0.156
#> TCGA-08-0524-01A-01 1 0.5842 0.8684 0.860 0.140
#> TCGA-12-0616-01A-01 1 0.0376 0.8770 0.996 0.004
#> TCGA-12-0618-01A-01 1 0.0376 0.8778 0.996 0.004
#> TCGA-02-0089-01A-01 2 0.4161 0.8803 0.084 0.916
#> TCGA-02-0113-01A-01 1 0.6623 0.8687 0.828 0.172
#> TCGA-02-0115-01A-01 1 0.8386 0.7901 0.732 0.268
#> TCGA-02-0451-01A-01 2 0.7139 0.7647 0.196 0.804
#> TCGA-06-0132-01A-02 1 0.0938 0.8788 0.988 0.012
#> TCGA-06-0133-01A-02 1 0.0376 0.8770 0.996 0.004
#> TCGA-06-0138-01A-02 1 0.0376 0.8770 0.996 0.004
#> TCGA-06-0160-01A-01 1 0.0000 0.8760 1.000 0.000
#> TCGA-06-0162-01A-01 1 0.0376 0.8770 0.996 0.004
#> TCGA-06-0167-01A-01 1 0.0000 0.8760 1.000 0.000
#> TCGA-06-0171-01A-02 1 0.0376 0.8770 0.996 0.004
#> TCGA-06-0173-01A-01 1 0.6343 0.8629 0.840 0.160
#> TCGA-06-0179-01A-02 1 0.0376 0.8770 0.996 0.004
#> TCGA-06-0182-01A-01 1 0.0376 0.8770 0.996 0.004
#> TCGA-06-0185-01A-01 1 0.3274 0.8780 0.940 0.060
#> TCGA-06-0195-01B-01 1 0.0000 0.8760 1.000 0.000
#> TCGA-06-0208-01B-01 1 0.0376 0.8770 0.996 0.004
#> TCGA-06-0214-01A-02 1 0.6438 0.8613 0.836 0.164
#> TCGA-06-0219-01A-01 1 0.0376 0.8770 0.996 0.004
#> TCGA-06-0221-01A-01 1 0.0376 0.8770 0.996 0.004
#> TCGA-06-0237-01A-02 1 0.0376 0.8770 0.996 0.004
#> TCGA-06-0240-01A-02 1 0.0376 0.8770 0.996 0.004
#> TCGA-08-0349-01A-01 1 0.0672 0.8784 0.992 0.008
#> TCGA-08-0380-01A-01 1 0.1414 0.8802 0.980 0.020
#> TCGA-08-0386-01A-01 1 0.7453 0.8450 0.788 0.212
#> TCGA-08-0520-01A-01 1 0.3274 0.8780 0.940 0.060
#> TCGA-02-0007-01A-01 1 0.7453 0.8450 0.788 0.212
#> TCGA-02-0009-01A-01 1 0.7453 0.8450 0.788 0.212
#> TCGA-02-0016-01A-01 1 0.4431 0.8817 0.908 0.092
#> TCGA-02-0021-01A-01 1 0.7453 0.8450 0.788 0.212
#> TCGA-02-0023-01B-01 1 0.3274 0.8780 0.940 0.060
#> TCGA-02-0027-01A-01 1 0.7139 0.8515 0.804 0.196
#> TCGA-02-0038-01A-01 1 0.9775 0.5404 0.588 0.412
#> TCGA-02-0043-01A-01 1 0.7453 0.8450 0.788 0.212
#> TCGA-02-0070-01A-01 1 0.7139 0.8520 0.804 0.196
#> TCGA-02-0102-01A-01 1 0.7453 0.8450 0.788 0.212
#> TCGA-02-0260-01A-03 1 0.3274 0.8791 0.940 0.060
#> TCGA-02-0269-01B-01 1 0.3114 0.8782 0.944 0.056
#> TCGA-02-0285-01A-01 1 0.7056 0.8546 0.808 0.192
#> TCGA-02-0289-01A-01 1 0.3274 0.8791 0.940 0.060
#> TCGA-02-0290-01A-01 1 0.3274 0.8780 0.940 0.060
#> TCGA-02-0317-01A-01 1 0.3274 0.8780 0.940 0.060
#> TCGA-02-0333-01A-02 1 0.3114 0.8782 0.944 0.056
#> TCGA-02-0422-01A-01 1 0.7139 0.8520 0.804 0.196
#> TCGA-02-0430-01A-01 1 0.7453 0.8450 0.788 0.212
#> TCGA-06-0125-01A-01 1 0.7453 0.8450 0.788 0.212
#> TCGA-06-0126-01A-01 1 0.7139 0.8515 0.804 0.196
#> TCGA-06-0137-01A-03 1 0.6801 0.8603 0.820 0.180
#> TCGA-06-0145-01A-04 2 0.8327 0.5796 0.264 0.736
#> TCGA-06-0148-01A-01 1 0.3431 0.8785 0.936 0.064
#> TCGA-06-0187-01A-01 2 0.3431 0.8996 0.064 0.936
#> TCGA-06-0211-01B-01 1 0.5408 0.8815 0.876 0.124
#> TCGA-06-0402-01A-01 1 0.7453 0.8450 0.788 0.212
#> TCGA-08-0246-01A-01 2 0.2948 0.9198 0.052 0.948
#> TCGA-08-0354-01A-01 1 0.3274 0.8780 0.940 0.060
#> TCGA-08-0355-01A-01 1 0.3274 0.8780 0.940 0.060
#> TCGA-08-0357-01A-01 1 0.7139 0.8520 0.804 0.196
#> TCGA-08-0358-01A-01 1 0.3274 0.8780 0.940 0.060
#> TCGA-08-0375-01A-01 1 0.7056 0.8533 0.808 0.192
#> TCGA-08-0511-01A-01 2 0.8861 0.4852 0.304 0.696
#> TCGA-08-0514-01A-01 2 0.5294 0.8374 0.120 0.880
#> TCGA-08-0518-01A-01 1 0.7453 0.8450 0.788 0.212
#> TCGA-08-0529-01A-02 1 0.7219 0.8500 0.800 0.200
#> TCGA-08-0531-01A-01 1 0.7139 0.8520 0.804 0.196
#> TCGA-02-0057-01A-01 2 0.2236 0.9303 0.036 0.964
#> TCGA-02-0004-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.2423 0.9220 0.040 0.960
#> TCGA-02-0025-01A-01 1 0.7602 0.7430 0.780 0.220
#> TCGA-02-0033-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.1184 0.9386 0.016 0.984
#> TCGA-02-0039-01A-01 1 0.9963 0.3158 0.536 0.464
#> TCGA-02-0051-01A-01 1 0.9000 0.7157 0.684 0.316
#> TCGA-02-0054-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.2778 0.9149 0.048 0.952
#> TCGA-02-0059-01A-01 1 0.8443 0.7500 0.728 0.272
#> TCGA-02-0064-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.4939 0.8508 0.108 0.892
#> TCGA-02-0079-01A-03 1 0.3274 0.8780 0.940 0.060
#> TCGA-02-0085-01A-01 2 0.1414 0.9361 0.020 0.980
#> TCGA-02-0086-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.1184 0.9375 0.016 0.984
#> TCGA-02-0106-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-02-0111-01A-01 1 0.9983 0.3577 0.524 0.476
#> TCGA-02-0326-01A-01 1 0.3274 0.8780 0.940 0.060
#> TCGA-02-0337-01A-01 1 0.9248 0.5857 0.660 0.340
#> TCGA-06-0122-01A-01 1 0.9044 0.7241 0.680 0.320
#> TCGA-06-0124-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.1414 0.9350 0.020 0.980
#> TCGA-06-0143-01A-01 1 0.8861 0.7360 0.696 0.304
#> TCGA-06-0147-01A-01 2 0.1184 0.9386 0.016 0.984
#> TCGA-06-0149-01A-05 1 0.8016 0.7069 0.756 0.244
#> TCGA-06-0152-01A-02 1 0.3274 0.8780 0.940 0.060
#> TCGA-06-0154-01A-02 2 0.1184 0.9386 0.016 0.984
#> TCGA-06-0164-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9422 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.2236 0.9307 0.036 0.964
#> TCGA-06-0189-01A-05 1 0.9286 0.6690 0.656 0.344
#> TCGA-06-0190-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.9795 0.0126 0.416 0.584
#> TCGA-06-0210-01A-01 2 0.1184 0.9386 0.016 0.984
#> TCGA-06-0397-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.1184 0.9386 0.016 0.984
#> TCGA-06-0412-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9422 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.1184 0.9386 0.016 0.984
#> TCGA-08-0346-01A-01 2 0.1414 0.9361 0.020 0.980
#> TCGA-08-0352-01A-01 2 0.7883 0.6709 0.236 0.764
#> TCGA-08-0360-01A-01 2 0.1184 0.9386 0.016 0.984
#> TCGA-08-0390-01A-01 1 0.7376 0.7859 0.792 0.208
#> TCGA-08-0392-01A-01 1 0.3274 0.8780 0.940 0.060
#> TCGA-08-0509-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9422 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.1184 0.9386 0.016 0.984
#> TCGA-12-0620-01A-01 1 0.4690 0.8629 0.900 0.100
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0848 0.7324 0.984 0.008 0.008
#> TCGA-02-0010-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-02-0011-01B-01 1 0.6155 0.1631 0.664 0.008 0.328
#> TCGA-02-0014-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-02-0024-01B-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-02-0026-01B-01 1 0.5497 0.2781 0.708 0.000 0.292
#> TCGA-02-0028-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-02-0046-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-02-0047-01A-01 2 0.8262 0.4089 0.276 0.608 0.116
#> TCGA-02-0048-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-02-0060-01A-01 3 0.6460 0.4935 0.440 0.004 0.556
#> TCGA-02-0069-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-02-0074-01A-01 1 0.0848 0.7324 0.984 0.008 0.008
#> TCGA-02-0080-01A-01 3 0.6675 0.5432 0.404 0.012 0.584
#> TCGA-02-0084-01A-03 3 0.5842 0.6865 0.036 0.196 0.768
#> TCGA-02-0087-01A-01 3 0.6047 0.6479 0.312 0.008 0.680
#> TCGA-02-0104-01A-01 3 0.4235 0.7290 0.176 0.000 0.824
#> TCGA-02-0114-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-02-0281-01A-01 1 0.5650 0.2227 0.688 0.000 0.312
#> TCGA-02-0321-01A-01 3 0.5884 0.6963 0.064 0.148 0.788
#> TCGA-02-0325-01A-01 3 0.8645 0.4888 0.300 0.132 0.568
#> TCGA-02-0338-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-02-0339-01A-01 3 0.6286 0.4598 0.464 0.000 0.536
#> TCGA-02-0432-01A-02 3 0.6432 0.5178 0.428 0.004 0.568
#> TCGA-02-0439-01A-01 3 0.7169 0.5294 0.404 0.028 0.568
#> TCGA-02-0440-01A-01 1 0.0848 0.7324 0.984 0.008 0.008
#> TCGA-02-0446-01A-01 2 0.6686 0.3167 0.372 0.612 0.016
#> TCGA-06-0128-01A-01 3 0.6672 0.4240 0.472 0.008 0.520
#> TCGA-06-0129-01A-01 1 0.0848 0.7324 0.984 0.008 0.008
#> TCGA-06-0146-01A-01 3 0.6495 0.4623 0.460 0.004 0.536
#> TCGA-06-0156-01A-01 1 0.7885 0.3844 0.580 0.352 0.068
#> TCGA-06-0166-01A-01 2 0.9736 -0.0614 0.356 0.416 0.228
#> TCGA-06-0174-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-06-0177-01A-01 3 0.6509 0.4274 0.472 0.004 0.524
#> TCGA-06-0238-01A-02 3 0.3851 0.7317 0.136 0.004 0.860
#> TCGA-06-0241-01A-02 1 0.4531 0.5340 0.824 0.008 0.168
#> TCGA-06-0410-01A-01 3 0.4702 0.7184 0.212 0.000 0.788
#> TCGA-06-0413-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-06-0414-01A-01 1 0.3826 0.6068 0.868 0.008 0.124
#> TCGA-06-0646-01A-01 2 0.7935 0.4865 0.236 0.648 0.116
#> TCGA-06-0648-01A-01 3 0.6095 0.5683 0.392 0.000 0.608
#> TCGA-08-0245-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-08-0344-01A-01 3 0.6280 0.4680 0.460 0.000 0.540
#> TCGA-08-0347-01A-01 2 0.8440 0.4468 0.184 0.620 0.196
#> TCGA-08-0348-01A-01 1 0.6948 -0.3329 0.512 0.016 0.472
#> TCGA-08-0350-01A-01 3 0.6359 0.5952 0.364 0.008 0.628
#> TCGA-08-0353-01A-01 1 0.2384 0.7053 0.936 0.056 0.008
#> TCGA-08-0359-01A-01 3 0.6763 0.4956 0.436 0.012 0.552
#> TCGA-08-0385-01A-01 3 0.6154 0.5468 0.408 0.000 0.592
#> TCGA-08-0517-01A-01 1 0.0848 0.7324 0.984 0.008 0.008
#> TCGA-08-0524-01A-01 1 0.0424 0.7345 0.992 0.008 0.000
#> TCGA-12-0616-01A-01 3 0.4047 0.7314 0.148 0.004 0.848
#> TCGA-12-0618-01A-01 3 0.6286 0.4598 0.464 0.000 0.536
#> TCGA-02-0089-01A-01 2 0.0237 0.8463 0.000 0.996 0.004
#> TCGA-02-0113-01A-01 2 0.6282 0.3869 0.004 0.612 0.384
#> TCGA-02-0115-01A-01 2 0.2297 0.8208 0.020 0.944 0.036
#> TCGA-02-0451-01A-01 2 0.4514 0.6849 0.156 0.832 0.012
#> TCGA-06-0132-01A-02 3 0.5442 0.7318 0.132 0.056 0.812
#> TCGA-06-0133-01A-02 3 0.3983 0.7311 0.144 0.004 0.852
#> TCGA-06-0138-01A-02 3 0.3983 0.7311 0.144 0.004 0.852
#> TCGA-06-0160-01A-01 3 0.4399 0.7265 0.188 0.000 0.812
#> TCGA-06-0162-01A-01 3 0.3983 0.7311 0.144 0.004 0.852
#> TCGA-06-0167-01A-01 3 0.4291 0.7282 0.180 0.000 0.820
#> TCGA-06-0171-01A-02 3 0.3983 0.7311 0.144 0.004 0.852
#> TCGA-06-0173-01A-01 2 0.9614 -0.0141 0.356 0.436 0.208
#> TCGA-06-0179-01A-02 3 0.5330 0.7318 0.144 0.044 0.812
#> TCGA-06-0182-01A-01 3 0.3983 0.7311 0.144 0.004 0.852
#> TCGA-06-0185-01A-01 3 0.4121 0.6901 0.000 0.168 0.832
#> TCGA-06-0195-01B-01 3 0.4291 0.7285 0.180 0.000 0.820
#> TCGA-06-0208-01B-01 3 0.3983 0.7311 0.144 0.004 0.852
#> TCGA-06-0214-01A-02 2 0.5178 0.6661 0.164 0.808 0.028
#> TCGA-06-0219-01A-01 3 0.3983 0.7311 0.144 0.004 0.852
#> TCGA-06-0221-01A-01 3 0.3983 0.7311 0.144 0.004 0.852
#> TCGA-06-0237-01A-02 3 0.3983 0.7311 0.144 0.004 0.852
#> TCGA-06-0240-01A-02 3 0.3983 0.7311 0.144 0.004 0.852
#> TCGA-08-0349-01A-01 3 0.5970 0.7292 0.160 0.060 0.780
#> TCGA-08-0380-01A-01 3 0.5954 0.7287 0.116 0.092 0.792
#> TCGA-08-0386-01A-01 1 0.5619 0.5718 0.744 0.244 0.012
#> TCGA-08-0520-01A-01 3 0.4164 0.6963 0.008 0.144 0.848
#> TCGA-02-0007-01A-01 1 0.6129 0.5185 0.700 0.284 0.016
#> TCGA-02-0009-01A-01 1 0.7069 0.1456 0.508 0.472 0.020
#> TCGA-02-0016-01A-01 3 0.8749 0.4791 0.300 0.140 0.560
#> TCGA-02-0021-01A-01 2 0.6683 -0.1015 0.492 0.500 0.008
#> TCGA-02-0023-01B-01 3 0.3816 0.6974 0.000 0.148 0.852
#> TCGA-02-0027-01A-01 2 0.8814 -0.0657 0.404 0.480 0.116
#> TCGA-02-0038-01A-01 2 0.0661 0.8430 0.004 0.988 0.008
#> TCGA-02-0043-01A-01 1 0.7069 0.1456 0.508 0.472 0.020
#> TCGA-02-0070-01A-01 2 0.8637 0.4004 0.152 0.588 0.260
#> TCGA-02-0102-01A-01 1 0.7293 0.1277 0.496 0.476 0.028
#> TCGA-02-0260-01A-03 3 0.5397 0.5477 0.280 0.000 0.720
#> TCGA-02-0269-01B-01 3 0.4887 0.6141 0.228 0.000 0.772
#> TCGA-02-0285-01A-01 3 0.7123 0.4584 0.032 0.364 0.604
#> TCGA-02-0289-01A-01 3 0.5058 0.5958 0.244 0.000 0.756
#> TCGA-02-0290-01A-01 3 0.1643 0.7005 0.000 0.044 0.956
#> TCGA-02-0317-01A-01 3 0.1529 0.7020 0.040 0.000 0.960
#> TCGA-02-0333-01A-02 3 0.3816 0.6808 0.148 0.000 0.852
#> TCGA-02-0422-01A-01 2 0.4165 0.7761 0.048 0.876 0.076
#> TCGA-02-0430-01A-01 1 0.7074 0.1213 0.500 0.480 0.020
#> TCGA-06-0125-01A-01 1 0.7289 0.1502 0.504 0.468 0.028
#> TCGA-06-0126-01A-01 2 0.8460 -0.1184 0.440 0.472 0.088
#> TCGA-06-0137-01A-03 3 0.9787 0.1978 0.320 0.252 0.428
#> TCGA-06-0145-01A-04 2 0.4700 0.6698 0.180 0.812 0.008
#> TCGA-06-0148-01A-01 3 0.5315 0.6253 0.216 0.012 0.772
#> TCGA-06-0187-01A-01 2 0.0424 0.8445 0.000 0.992 0.008
#> TCGA-06-0211-01B-01 1 0.9022 -0.0753 0.480 0.136 0.384
#> TCGA-06-0402-01A-01 1 0.6680 0.1146 0.508 0.484 0.008
#> TCGA-08-0246-01A-01 2 0.0237 0.8463 0.000 0.996 0.004
#> TCGA-08-0354-01A-01 3 0.4228 0.6955 0.008 0.148 0.844
#> TCGA-08-0355-01A-01 3 0.4178 0.6885 0.000 0.172 0.828
#> TCGA-08-0357-01A-01 2 0.8862 0.3519 0.164 0.564 0.272
#> TCGA-08-0358-01A-01 3 0.0000 0.6902 0.000 0.000 1.000
#> TCGA-08-0375-01A-01 3 0.9131 0.2703 0.396 0.144 0.460
#> TCGA-08-0511-01A-01 2 0.3454 0.7639 0.104 0.888 0.008
#> TCGA-08-0514-01A-01 2 0.0848 0.8410 0.008 0.984 0.008
#> TCGA-08-0518-01A-01 2 0.7140 0.3355 0.328 0.632 0.040
#> TCGA-08-0529-01A-02 2 0.6109 0.6248 0.192 0.760 0.048
#> TCGA-08-0531-01A-01 2 0.8452 0.2788 0.096 0.532 0.372
#> TCGA-02-0057-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0004-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0006-01B-01 2 0.2066 0.7986 0.060 0.940 0.000
#> TCGA-02-0025-01A-01 3 0.4931 0.6567 0.000 0.232 0.768
#> TCGA-02-0033-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0039-01A-01 2 0.4235 0.6677 0.000 0.824 0.176
#> TCGA-02-0051-01A-01 2 0.6154 0.4150 0.000 0.592 0.408
#> TCGA-02-0054-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0059-01A-01 3 0.4931 0.6561 0.000 0.232 0.768
#> TCGA-02-0064-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0079-01A-03 3 0.2356 0.7055 0.000 0.072 0.928
#> TCGA-02-0085-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0086-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0099-01A-01 2 0.0424 0.8445 0.000 0.992 0.008
#> TCGA-02-0106-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-02-0111-01A-01 3 0.6260 0.3499 0.000 0.448 0.552
#> TCGA-02-0326-01A-01 3 0.0592 0.6942 0.000 0.012 0.988
#> TCGA-02-0337-01A-01 3 0.6305 0.1647 0.000 0.484 0.516
#> TCGA-06-0122-01A-01 2 0.1129 0.8362 0.020 0.976 0.004
#> TCGA-06-0124-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0139-01A-01 2 0.0424 0.8448 0.000 0.992 0.008
#> TCGA-06-0143-01A-01 2 0.4712 0.7383 0.108 0.848 0.044
#> TCGA-06-0147-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0149-01A-05 2 0.6192 0.0309 0.000 0.580 0.420
#> TCGA-06-0152-01A-02 3 0.4121 0.6900 0.000 0.168 0.832
#> TCGA-06-0154-01A-02 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0175-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0184-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0189-01A-05 3 0.5706 0.5763 0.000 0.320 0.680
#> TCGA-06-0190-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0197-01A-02 2 0.1753 0.8224 0.000 0.952 0.048
#> TCGA-06-0210-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0412-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-08-0352-01A-01 2 0.1031 0.8340 0.024 0.976 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-08-0390-01A-01 3 0.4974 0.6544 0.000 0.236 0.764
#> TCGA-08-0392-01A-01 3 0.2173 0.7008 0.008 0.048 0.944
#> TCGA-08-0509-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.8478 0.000 1.000 0.000
#> TCGA-12-0620-01A-01 3 0.4702 0.6685 0.000 0.212 0.788
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.1022 0.8677 0.968 0.000 0.000 0.032
#> TCGA-02-0010-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0047-01A-01 2 0.4244 0.7582 0.160 0.804 0.000 0.036
#> TCGA-02-0048-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0060-01A-01 1 0.7454 0.0248 0.496 0.084 0.388 0.032
#> TCGA-02-0069-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.1022 0.8677 0.968 0.000 0.000 0.032
#> TCGA-02-0080-01A-01 3 0.4290 0.8029 0.164 0.036 0.800 0.000
#> TCGA-02-0084-01A-03 3 0.4397 0.7444 0.012 0.168 0.800 0.020
#> TCGA-02-0087-01A-01 3 0.4909 0.7978 0.128 0.040 0.800 0.032
#> TCGA-02-0104-01A-01 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-02-0114-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 2 0.3494 0.7761 0.004 0.824 0.172 0.000
#> TCGA-02-0325-01A-01 3 0.3402 0.7412 0.004 0.164 0.832 0.000
#> TCGA-02-0338-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.2814 0.7602 0.868 0.000 0.132 0.000
#> TCGA-02-0432-01A-02 3 0.3610 0.7780 0.200 0.000 0.800 0.000
#> TCGA-02-0439-01A-01 2 0.7929 0.1618 0.144 0.504 0.320 0.032
#> TCGA-02-0440-01A-01 1 0.1022 0.8677 0.968 0.000 0.000 0.032
#> TCGA-02-0446-01A-01 2 0.4244 0.7582 0.160 0.804 0.000 0.036
#> TCGA-06-0128-01A-01 1 0.1022 0.8677 0.968 0.000 0.000 0.032
#> TCGA-06-0129-01A-01 1 0.1022 0.8677 0.968 0.000 0.000 0.032
#> TCGA-06-0146-01A-01 3 0.4164 0.7175 0.264 0.000 0.736 0.000
#> TCGA-06-0156-01A-01 1 0.3907 0.7324 0.828 0.140 0.000 0.032
#> TCGA-06-0166-01A-01 2 0.4579 0.7206 0.200 0.768 0.000 0.032
#> TCGA-06-0174-01A-01 1 0.0817 0.8700 0.976 0.000 0.000 0.024
#> TCGA-06-0177-01A-01 1 0.4152 0.7192 0.808 0.000 0.160 0.032
#> TCGA-06-0238-01A-02 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.1022 0.8677 0.968 0.000 0.000 0.032
#> TCGA-06-0410-01A-01 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0413-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.1022 0.8677 0.968 0.000 0.000 0.032
#> TCGA-06-0646-01A-01 2 0.4199 0.7569 0.164 0.804 0.000 0.032
#> TCGA-06-0648-01A-01 3 0.4204 0.7685 0.192 0.000 0.788 0.020
#> TCGA-08-0245-01A-01 1 0.0188 0.8740 0.996 0.000 0.000 0.004
#> TCGA-08-0344-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 2 0.1022 0.9112 0.000 0.968 0.000 0.032
#> TCGA-08-0348-01A-01 1 0.1356 0.8653 0.960 0.008 0.000 0.032
#> TCGA-08-0350-01A-01 3 0.4673 0.7838 0.156 0.016 0.796 0.032
#> TCGA-08-0353-01A-01 1 0.1739 0.8602 0.952 0.016 0.024 0.008
#> TCGA-08-0359-01A-01 2 0.5085 0.6397 0.260 0.708 0.000 0.032
#> TCGA-08-0385-01A-01 3 0.4679 0.5711 0.352 0.000 0.648 0.000
#> TCGA-08-0517-01A-01 1 0.1022 0.8677 0.968 0.000 0.000 0.032
#> TCGA-08-0524-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 4 0.2589 0.8027 0.116 0.000 0.000 0.884
#> TCGA-12-0618-01A-01 1 0.0000 0.8746 1.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0113-01A-01 2 0.1022 0.9123 0.000 0.968 0.032 0.000
#> TCGA-02-0115-01A-01 2 0.2032 0.8912 0.028 0.936 0.000 0.036
#> TCGA-02-0451-01A-01 2 0.4244 0.7582 0.160 0.804 0.000 0.036
#> TCGA-06-0132-01A-02 2 0.3751 0.7545 0.004 0.800 0.000 0.196
#> TCGA-06-0133-01A-02 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0138-01A-02 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0160-01A-01 4 0.3528 0.7315 0.000 0.000 0.192 0.808
#> TCGA-06-0162-01A-01 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0167-01A-01 4 0.2345 0.8432 0.000 0.000 0.100 0.900
#> TCGA-06-0171-01A-02 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0173-01A-01 2 0.4692 0.7080 0.212 0.756 0.000 0.032
#> TCGA-06-0179-01A-02 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0182-01A-01 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0185-01A-01 4 0.4244 0.7016 0.000 0.160 0.036 0.804
#> TCGA-06-0195-01B-01 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0208-01B-01 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.4244 0.7582 0.160 0.804 0.000 0.036
#> TCGA-06-0219-01A-01 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0221-01A-01 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0237-01A-02 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-06-0240-01A-02 4 0.0000 0.9250 0.000 0.000 0.000 1.000
#> TCGA-08-0349-01A-01 2 0.4244 0.7582 0.160 0.804 0.000 0.036
#> TCGA-08-0380-01A-01 2 0.3245 0.8448 0.064 0.880 0.000 0.056
#> TCGA-08-0386-01A-01 1 0.4199 0.7225 0.804 0.164 0.032 0.000
#> TCGA-08-0520-01A-01 4 0.4332 0.6993 0.000 0.160 0.040 0.800
#> TCGA-02-0007-01A-01 1 0.4199 0.7225 0.804 0.164 0.032 0.000
#> TCGA-02-0009-01A-01 1 0.4199 0.7225 0.804 0.164 0.032 0.000
#> TCGA-02-0016-01A-01 2 0.6402 0.4574 0.108 0.624 0.268 0.000
#> TCGA-02-0021-01A-01 2 0.5645 0.3291 0.364 0.604 0.032 0.000
#> TCGA-02-0023-01B-01 3 0.1474 0.8315 0.000 0.052 0.948 0.000
#> TCGA-02-0027-01A-01 2 0.4060 0.7855 0.140 0.828 0.020 0.012
#> TCGA-02-0038-01A-01 2 0.0188 0.9262 0.004 0.996 0.000 0.000
#> TCGA-02-0043-01A-01 1 0.4244 0.7190 0.800 0.168 0.032 0.000
#> TCGA-02-0070-01A-01 2 0.1022 0.9123 0.000 0.968 0.032 0.000
#> TCGA-02-0102-01A-01 1 0.5815 0.2870 0.540 0.428 0.032 0.000
#> TCGA-02-0260-01A-03 3 0.0000 0.8478 0.000 0.000 1.000 0.000
#> TCGA-02-0269-01B-01 3 0.0000 0.8478 0.000 0.000 1.000 0.000
#> TCGA-02-0285-01A-01 2 0.1022 0.9123 0.000 0.968 0.032 0.000
#> TCGA-02-0289-01A-01 3 0.0000 0.8478 0.000 0.000 1.000 0.000
#> TCGA-02-0290-01A-01 3 0.1557 0.8231 0.000 0.056 0.944 0.000
#> TCGA-02-0317-01A-01 3 0.0000 0.8478 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 3 0.0000 0.8478 0.000 0.000 1.000 0.000
#> TCGA-02-0422-01A-01 2 0.1022 0.9123 0.000 0.968 0.032 0.000
#> TCGA-02-0430-01A-01 2 0.5861 -0.1032 0.480 0.488 0.032 0.000
#> TCGA-06-0125-01A-01 1 0.4199 0.7225 0.804 0.164 0.032 0.000
#> TCGA-06-0126-01A-01 1 0.5085 0.6066 0.708 0.260 0.032 0.000
#> TCGA-06-0137-01A-03 2 0.5948 0.6096 0.160 0.696 0.144 0.000
#> TCGA-06-0145-01A-04 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0148-01A-01 3 0.0000 0.8478 0.000 0.000 1.000 0.000
#> TCGA-06-0187-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0211-01B-01 1 0.3638 0.7673 0.848 0.120 0.032 0.000
#> TCGA-06-0402-01A-01 1 0.4995 0.6231 0.720 0.248 0.032 0.000
#> TCGA-08-0246-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-08-0354-01A-01 4 0.4370 0.7035 0.000 0.156 0.044 0.800
#> TCGA-08-0355-01A-01 3 0.3219 0.7412 0.000 0.164 0.836 0.000
#> TCGA-08-0357-01A-01 2 0.1022 0.9123 0.000 0.968 0.032 0.000
#> TCGA-08-0358-01A-01 3 0.0000 0.8478 0.000 0.000 1.000 0.000
#> TCGA-08-0375-01A-01 1 0.4244 0.7190 0.800 0.168 0.032 0.000
#> TCGA-08-0511-01A-01 2 0.1022 0.9123 0.000 0.968 0.032 0.000
#> TCGA-08-0514-01A-01 2 0.1022 0.9123 0.000 0.968 0.032 0.000
#> TCGA-08-0518-01A-01 2 0.1022 0.9123 0.000 0.968 0.032 0.000
#> TCGA-08-0529-01A-02 2 0.1022 0.9123 0.000 0.968 0.032 0.000
#> TCGA-08-0531-01A-01 2 0.1211 0.9088 0.000 0.960 0.040 0.000
#> TCGA-02-0057-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0004-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0006-01B-01 2 0.1978 0.8752 0.068 0.928 0.000 0.004
#> TCGA-02-0025-01A-01 2 0.4431 0.5208 0.000 0.696 0.304 0.000
#> TCGA-02-0033-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.2081 0.8789 0.000 0.916 0.084 0.000
#> TCGA-02-0054-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0064-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0075-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0079-01A-03 3 0.0000 0.8478 0.000 0.000 1.000 0.000
#> TCGA-02-0085-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0086-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0099-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0106-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-02-0326-01A-01 3 0.0000 0.8478 0.000 0.000 1.000 0.000
#> TCGA-02-0337-01A-01 2 0.0336 0.9244 0.000 0.992 0.008 0.000
#> TCGA-06-0122-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0124-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0143-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0147-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0152-01A-02 3 0.3266 0.7378 0.000 0.168 0.832 0.000
#> TCGA-06-0154-01A-02 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0175-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0189-01A-05 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0397-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0412-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-08-0352-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-08-0360-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-08-0392-01A-01 4 0.3937 0.7787 0.000 0.012 0.188 0.800
#> TCGA-08-0509-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-08-0510-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-08-0512-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-08-0522-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.0000 0.9284 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.0771 0.86970 0.976 0.020 0.004 0.000 0.000
#> TCGA-02-0010-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0290 0.87058 0.992 0.000 0.008 0.000 0.000
#> TCGA-02-0014-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0566 0.87136 0.984 0.012 0.004 0.000 0.000
#> TCGA-02-0047-01A-01 3 0.6244 0.33118 0.128 0.248 0.600 0.024 0.000
#> TCGA-02-0048-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0060-01A-01 5 0.6393 0.50890 0.292 0.000 0.164 0.008 0.536
#> TCGA-02-0069-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0771 0.86970 0.976 0.020 0.004 0.000 0.000
#> TCGA-02-0080-01A-01 5 0.3772 0.79218 0.172 0.000 0.036 0.000 0.792
#> TCGA-02-0084-01A-03 5 0.3965 0.78360 0.016 0.020 0.160 0.004 0.800
#> TCGA-02-0087-01A-01 5 0.4266 0.80585 0.108 0.000 0.072 0.020 0.800
#> TCGA-02-0104-01A-01 4 0.1410 0.88936 0.060 0.000 0.000 0.940 0.000
#> TCGA-02-0114-01A-01 1 0.0566 0.87136 0.984 0.012 0.004 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0321-01A-01 5 0.5005 0.51327 0.004 0.028 0.388 0.000 0.580
#> TCGA-02-0325-01A-01 5 0.3160 0.76791 0.004 0.000 0.188 0.000 0.808
#> TCGA-02-0338-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.3398 0.61040 0.780 0.000 0.004 0.000 0.216
#> TCGA-02-0432-01A-02 5 0.3388 0.77197 0.200 0.000 0.008 0.000 0.792
#> TCGA-02-0439-01A-01 5 0.5841 0.70918 0.104 0.000 0.236 0.020 0.640
#> TCGA-02-0440-01A-01 1 0.0771 0.86970 0.976 0.020 0.004 0.000 0.000
#> TCGA-02-0446-01A-01 3 0.5622 0.43276 0.140 0.148 0.688 0.024 0.000
#> TCGA-06-0128-01A-01 1 0.1485 0.85929 0.948 0.020 0.032 0.000 0.000
#> TCGA-06-0129-01A-01 1 0.0771 0.86970 0.976 0.020 0.004 0.000 0.000
#> TCGA-06-0146-01A-01 5 0.3821 0.75668 0.216 0.000 0.020 0.000 0.764
#> TCGA-06-0156-01A-01 1 0.4254 0.73575 0.768 0.020 0.188 0.024 0.000
#> TCGA-06-0166-01A-01 1 0.6593 0.24108 0.504 0.124 0.348 0.024 0.000
#> TCGA-06-0174-01A-01 1 0.0771 0.86970 0.976 0.020 0.004 0.000 0.000
#> TCGA-06-0177-01A-01 1 0.4701 0.58811 0.720 0.000 0.076 0.000 0.204
#> TCGA-06-0238-01A-02 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0241-01A-02 1 0.0771 0.86970 0.976 0.020 0.004 0.000 0.000
#> TCGA-06-0410-01A-01 4 0.1197 0.89756 0.048 0.000 0.000 0.952 0.000
#> TCGA-06-0413-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.0771 0.86970 0.976 0.020 0.004 0.000 0.000
#> TCGA-06-0646-01A-01 3 0.5455 0.43952 0.108 0.188 0.688 0.016 0.000
#> TCGA-06-0648-01A-01 5 0.3630 0.76784 0.204 0.000 0.016 0.000 0.780
#> TCGA-08-0245-01A-01 1 0.0451 0.87192 0.988 0.008 0.004 0.000 0.000
#> TCGA-08-0344-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0347-01A-01 3 0.2732 0.54237 0.000 0.160 0.840 0.000 0.000
#> TCGA-08-0348-01A-01 1 0.3438 0.76373 0.808 0.020 0.172 0.000 0.000
#> TCGA-08-0350-01A-01 5 0.4375 0.79697 0.148 0.000 0.056 0.016 0.780
#> TCGA-08-0353-01A-01 1 0.2660 0.77990 0.864 0.000 0.128 0.000 0.008
#> TCGA-08-0359-01A-01 1 0.7561 0.19762 0.416 0.048 0.396 0.024 0.116
#> TCGA-08-0385-01A-01 5 0.4184 0.67809 0.284 0.000 0.016 0.000 0.700
#> TCGA-08-0517-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 4 0.1121 0.89451 0.044 0.000 0.000 0.956 0.000
#> TCGA-12-0618-01A-01 1 0.0000 0.87324 1.000 0.000 0.000 0.000 0.000
#> TCGA-02-0089-01A-01 2 0.3895 0.47390 0.000 0.680 0.320 0.000 0.000
#> TCGA-02-0113-01A-01 2 0.4456 0.45010 0.000 0.660 0.320 0.000 0.020
#> TCGA-02-0115-01A-01 2 0.4288 0.46242 0.012 0.664 0.324 0.000 0.000
#> TCGA-02-0451-01A-01 2 0.6069 0.40154 0.088 0.588 0.300 0.024 0.000
#> TCGA-06-0132-01A-02 2 0.3454 0.44674 0.000 0.816 0.028 0.156 0.000
#> TCGA-06-0133-01A-02 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0138-01A-02 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0160-01A-01 4 0.4161 0.69158 0.040 0.000 0.000 0.752 0.208
#> TCGA-06-0162-01A-01 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0167-01A-01 4 0.3035 0.82296 0.032 0.000 0.000 0.856 0.112
#> TCGA-06-0171-01A-02 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0173-01A-01 1 0.6154 0.37824 0.556 0.084 0.336 0.024 0.000
#> TCGA-06-0179-01A-02 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0182-01A-01 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0185-01A-01 4 0.3870 0.73608 0.000 0.016 0.176 0.792 0.016
#> TCGA-06-0195-01B-01 4 0.0963 0.90452 0.036 0.000 0.000 0.964 0.000
#> TCGA-06-0208-01B-01 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0214-01A-02 2 0.6250 0.39834 0.120 0.592 0.264 0.024 0.000
#> TCGA-06-0219-01A-01 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0221-01A-01 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0237-01A-02 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-06-0240-01A-02 4 0.0000 0.92140 0.000 0.000 0.000 1.000 0.000
#> TCGA-08-0349-01A-01 2 0.6136 0.38622 0.124 0.616 0.236 0.024 0.000
#> TCGA-08-0380-01A-01 2 0.3918 0.48170 0.008 0.804 0.144 0.044 0.000
#> TCGA-08-0386-01A-01 1 0.4184 0.63501 0.700 0.000 0.284 0.000 0.016
#> TCGA-08-0520-01A-01 4 0.4119 0.74016 0.000 0.032 0.156 0.792 0.020
#> TCGA-02-0007-01A-01 1 0.4290 0.61797 0.680 0.000 0.304 0.000 0.016
#> TCGA-02-0009-01A-01 3 0.4451 0.13730 0.340 0.000 0.644 0.000 0.016
#> TCGA-02-0016-01A-01 3 0.5188 0.21654 0.060 0.000 0.612 0.000 0.328
#> TCGA-02-0021-01A-01 3 0.1626 0.53754 0.044 0.000 0.940 0.000 0.016
#> TCGA-02-0023-01B-01 5 0.0992 0.82215 0.000 0.008 0.024 0.000 0.968
#> TCGA-02-0027-01A-01 3 0.0865 0.54901 0.024 0.004 0.972 0.000 0.000
#> TCGA-02-0038-01A-01 3 0.3876 0.38594 0.000 0.316 0.684 0.000 0.000
#> TCGA-02-0043-01A-01 3 0.3562 0.40801 0.196 0.000 0.788 0.000 0.016
#> TCGA-02-0070-01A-01 3 0.1701 0.56473 0.000 0.048 0.936 0.000 0.016
#> TCGA-02-0102-01A-01 3 0.0798 0.54555 0.008 0.000 0.976 0.000 0.016
#> TCGA-02-0260-01A-03 5 0.0162 0.82186 0.000 0.000 0.004 0.000 0.996
#> TCGA-02-0269-01B-01 5 0.0162 0.82186 0.000 0.000 0.004 0.000 0.996
#> TCGA-02-0285-01A-01 3 0.4090 0.46764 0.000 0.268 0.716 0.000 0.016
#> TCGA-02-0289-01A-01 5 0.0162 0.82186 0.000 0.000 0.004 0.000 0.996
#> TCGA-02-0290-01A-01 5 0.0510 0.82118 0.000 0.016 0.000 0.000 0.984
#> TCGA-02-0317-01A-01 5 0.0000 0.82126 0.000 0.000 0.000 0.000 1.000
#> TCGA-02-0333-01A-02 5 0.0162 0.82186 0.000 0.000 0.004 0.000 0.996
#> TCGA-02-0422-01A-01 3 0.3630 0.52348 0.000 0.204 0.780 0.000 0.016
#> TCGA-02-0430-01A-01 3 0.4874 0.09970 0.388 0.008 0.588 0.000 0.016
#> TCGA-06-0125-01A-01 3 0.4014 0.35366 0.256 0.000 0.728 0.000 0.016
#> TCGA-06-0126-01A-01 3 0.1914 0.52020 0.060 0.000 0.924 0.000 0.016
#> TCGA-06-0137-01A-03 3 0.2278 0.51665 0.032 0.000 0.908 0.000 0.060
#> TCGA-06-0145-01A-04 3 0.1608 0.57107 0.000 0.072 0.928 0.000 0.000
#> TCGA-06-0148-01A-01 5 0.3274 0.64454 0.000 0.000 0.220 0.000 0.780
#> TCGA-06-0187-01A-01 3 0.2753 0.56938 0.000 0.136 0.856 0.000 0.008
#> TCGA-06-0211-01B-01 1 0.4265 0.64748 0.712 0.008 0.268 0.000 0.012
#> TCGA-06-0402-01A-01 3 0.4763 0.22338 0.352 0.008 0.624 0.000 0.016
#> TCGA-08-0246-01A-01 2 0.4307 0.11732 0.000 0.504 0.496 0.000 0.000
#> TCGA-08-0354-01A-01 4 0.4360 0.75334 0.000 0.052 0.128 0.792 0.028
#> TCGA-08-0355-01A-01 5 0.3489 0.76948 0.000 0.036 0.144 0.000 0.820
#> TCGA-08-0357-01A-01 3 0.3343 0.53607 0.000 0.172 0.812 0.000 0.016
#> TCGA-08-0358-01A-01 5 0.0290 0.82085 0.000 0.008 0.000 0.000 0.992
#> TCGA-08-0375-01A-01 1 0.4467 0.57835 0.640 0.000 0.344 0.000 0.016
#> TCGA-08-0511-01A-01 3 0.1845 0.56834 0.000 0.056 0.928 0.000 0.016
#> TCGA-08-0514-01A-01 3 0.3630 0.53333 0.000 0.204 0.780 0.000 0.016
#> TCGA-08-0518-01A-01 3 0.1862 0.55365 0.004 0.048 0.932 0.000 0.016
#> TCGA-08-0529-01A-02 3 0.3011 0.56143 0.000 0.140 0.844 0.000 0.016
#> TCGA-08-0531-01A-01 3 0.3934 0.47221 0.000 0.244 0.740 0.000 0.016
#> TCGA-02-0057-01A-01 3 0.3003 0.53579 0.000 0.188 0.812 0.000 0.000
#> TCGA-02-0004-01A-01 2 0.3003 0.57001 0.000 0.812 0.188 0.000 0.000
#> TCGA-02-0006-01B-01 3 0.4299 0.24095 0.004 0.388 0.608 0.000 0.000
#> TCGA-02-0025-01A-01 2 0.4920 0.17892 0.000 0.584 0.032 0.000 0.384
#> TCGA-02-0033-01A-01 3 0.4297 0.07613 0.000 0.472 0.528 0.000 0.000
#> TCGA-02-0034-01A-01 3 0.4210 0.23164 0.000 0.412 0.588 0.000 0.000
#> TCGA-02-0039-01A-01 2 0.3424 0.52932 0.000 0.760 0.240 0.000 0.000
#> TCGA-02-0051-01A-01 2 0.2006 0.52930 0.000 0.916 0.012 0.000 0.072
#> TCGA-02-0054-01A-01 3 0.3983 0.34300 0.000 0.340 0.660 0.000 0.000
#> TCGA-02-0055-01A-01 2 0.0794 0.57287 0.000 0.972 0.028 0.000 0.000
#> TCGA-02-0059-01A-01 2 0.0865 0.56882 0.000 0.972 0.024 0.000 0.004
#> TCGA-02-0064-01A-01 3 0.4074 0.30400 0.000 0.364 0.636 0.000 0.000
#> TCGA-02-0075-01A-01 3 0.3774 0.42137 0.000 0.296 0.704 0.000 0.000
#> TCGA-02-0079-01A-03 5 0.1197 0.80819 0.000 0.048 0.000 0.000 0.952
#> TCGA-02-0085-01A-01 3 0.4273 0.04676 0.000 0.448 0.552 0.000 0.000
#> TCGA-02-0086-01A-01 2 0.3177 0.56437 0.000 0.792 0.208 0.000 0.000
#> TCGA-02-0099-01A-01 3 0.2516 0.56850 0.000 0.140 0.860 0.000 0.000
#> TCGA-02-0106-01A-01 2 0.4219 0.23713 0.000 0.584 0.416 0.000 0.000
#> TCGA-02-0107-01A-01 2 0.2966 0.57225 0.000 0.816 0.184 0.000 0.000
#> TCGA-02-0111-01A-01 2 0.0794 0.57287 0.000 0.972 0.028 0.000 0.000
#> TCGA-02-0326-01A-01 5 0.0162 0.82113 0.000 0.004 0.000 0.000 0.996
#> TCGA-02-0337-01A-01 3 0.6796 -0.02728 0.000 0.316 0.380 0.000 0.304
#> TCGA-06-0122-01A-01 3 0.3109 0.51413 0.000 0.200 0.800 0.000 0.000
#> TCGA-06-0124-01A-01 3 0.4045 0.32123 0.000 0.356 0.644 0.000 0.000
#> TCGA-06-0130-01A-01 2 0.4305 0.02127 0.000 0.512 0.488 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0794 0.57287 0.000 0.972 0.028 0.000 0.000
#> TCGA-06-0143-01A-01 3 0.2020 0.57038 0.000 0.100 0.900 0.000 0.000
#> TCGA-06-0147-01A-01 3 0.4283 0.12187 0.000 0.456 0.544 0.000 0.000
#> TCGA-06-0149-01A-05 2 0.4192 0.27435 0.000 0.596 0.404 0.000 0.000
#> TCGA-06-0152-01A-02 5 0.3412 0.76618 0.000 0.028 0.152 0.000 0.820
#> TCGA-06-0154-01A-02 3 0.4300 0.07499 0.000 0.476 0.524 0.000 0.000
#> TCGA-06-0164-01A-01 2 0.4210 0.24679 0.000 0.588 0.412 0.000 0.000
#> TCGA-06-0175-01A-01 3 0.3336 0.51930 0.000 0.228 0.772 0.000 0.000
#> TCGA-06-0176-01A-03 2 0.4304 0.02416 0.000 0.516 0.484 0.000 0.000
#> TCGA-06-0184-01A-01 2 0.1965 0.55637 0.000 0.904 0.096 0.000 0.000
#> TCGA-06-0189-01A-05 2 0.0963 0.57316 0.000 0.964 0.036 0.000 0.000
#> TCGA-06-0190-01A-01 2 0.4305 0.01720 0.000 0.512 0.488 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.2852 0.57872 0.000 0.828 0.172 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0794 0.57287 0.000 0.972 0.028 0.000 0.000
#> TCGA-06-0210-01A-01 2 0.4256 0.25709 0.000 0.564 0.436 0.000 0.000
#> TCGA-06-0397-01A-01 3 0.4262 0.17853 0.000 0.440 0.560 0.000 0.000
#> TCGA-06-0409-01A-02 2 0.4268 0.16071 0.000 0.556 0.444 0.000 0.000
#> TCGA-06-0412-01A-01 3 0.4294 0.07176 0.000 0.468 0.532 0.000 0.000
#> TCGA-06-0644-01A-02 2 0.2929 0.57368 0.000 0.820 0.180 0.000 0.000
#> TCGA-06-0645-01A-01 2 0.4268 0.24936 0.000 0.556 0.444 0.000 0.000
#> TCGA-08-0346-01A-01 2 0.4278 0.13691 0.000 0.548 0.452 0.000 0.000
#> TCGA-08-0352-01A-01 3 0.4201 0.24760 0.000 0.408 0.592 0.000 0.000
#> TCGA-08-0360-01A-01 2 0.4300 0.06004 0.000 0.524 0.476 0.000 0.000
#> TCGA-08-0390-01A-01 2 0.1341 0.57002 0.000 0.944 0.056 0.000 0.000
#> TCGA-08-0392-01A-01 4 0.5466 0.68205 0.000 0.192 0.004 0.668 0.136
#> TCGA-08-0509-01A-01 2 0.4306 0.00411 0.000 0.508 0.492 0.000 0.000
#> TCGA-08-0510-01A-01 3 0.4101 0.29751 0.000 0.372 0.628 0.000 0.000
#> TCGA-08-0512-01A-01 3 0.4278 0.13935 0.000 0.452 0.548 0.000 0.000
#> TCGA-08-0522-01A-01 3 0.4219 0.22346 0.000 0.416 0.584 0.000 0.000
#> TCGA-12-0619-01A-01 3 0.4114 0.29002 0.000 0.376 0.624 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.5050 0.43362 0.000 0.700 0.120 0.000 0.180
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.1926 0.8332 0.912 0.000 0.020 0.000 0.000 0.068
#> TCGA-02-0010-01A-01 1 0.0260 0.8694 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0622 0.8664 0.980 0.000 0.012 0.000 0.008 0.000
#> TCGA-02-0014-01A-01 1 0.0260 0.8694 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0260 0.8694 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-02-0026-01B-01 1 0.0692 0.8643 0.976 0.000 0.020 0.000 0.000 0.004
#> TCGA-02-0028-01A-01 1 0.0260 0.8694 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0520 0.8639 0.984 0.000 0.008 0.000 0.000 0.008
#> TCGA-02-0047-01A-01 3 0.4415 0.6755 0.048 0.028 0.732 0.000 0.000 0.192
#> TCGA-02-0048-01A-01 1 0.0547 0.8679 0.980 0.000 0.020 0.000 0.000 0.000
#> TCGA-02-0060-01A-01 3 0.6361 0.2725 0.200 0.000 0.500 0.000 0.264 0.036
#> TCGA-02-0069-01A-01 1 0.0260 0.8694 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.2389 0.7889 0.864 0.000 0.008 0.000 0.000 0.128
#> TCGA-02-0080-01A-01 5 0.5125 0.7215 0.184 0.000 0.052 0.000 0.688 0.076
#> TCGA-02-0084-01A-03 5 0.4064 0.7498 0.008 0.096 0.064 0.000 0.800 0.032
#> TCGA-02-0087-01A-01 5 0.4047 0.7775 0.064 0.000 0.052 0.000 0.796 0.088
#> TCGA-02-0104-01A-01 4 0.2300 0.7912 0.144 0.000 0.000 0.856 0.000 0.000
#> TCGA-02-0114-01A-01 1 0.0547 0.8639 0.980 0.000 0.020 0.000 0.000 0.000
#> TCGA-02-0281-01A-01 1 0.0935 0.8581 0.964 0.000 0.032 0.000 0.000 0.004
#> TCGA-02-0321-01A-01 3 0.4605 0.2551 0.000 0.008 0.596 0.000 0.364 0.032
#> TCGA-02-0325-01A-01 5 0.4504 0.7214 0.008 0.004 0.204 0.000 0.716 0.068
#> TCGA-02-0338-01A-01 1 0.0260 0.8694 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.1767 0.8392 0.932 0.000 0.036 0.000 0.020 0.012
#> TCGA-02-0432-01A-02 5 0.5835 0.5403 0.312 0.000 0.052 0.000 0.556 0.080
#> TCGA-02-0439-01A-01 3 0.5593 0.4283 0.112 0.000 0.600 0.000 0.260 0.028
#> TCGA-02-0440-01A-01 1 0.4352 0.6513 0.724 0.000 0.148 0.000 0.000 0.128
#> TCGA-02-0446-01A-01 3 0.5646 0.6984 0.076 0.108 0.652 0.000 0.000 0.164
#> TCGA-06-0128-01A-01 3 0.5685 0.3722 0.372 0.008 0.492 0.000 0.000 0.128
#> TCGA-06-0129-01A-01 1 0.2389 0.7889 0.864 0.000 0.008 0.000 0.000 0.128
#> TCGA-06-0146-01A-01 1 0.5905 0.0163 0.532 0.000 0.052 0.000 0.336 0.080
#> TCGA-06-0156-01A-01 3 0.5262 0.6205 0.204 0.008 0.632 0.000 0.000 0.156
#> TCGA-06-0166-01A-01 3 0.4366 0.6698 0.072 0.012 0.732 0.000 0.000 0.184
#> TCGA-06-0174-01A-01 1 0.1334 0.8534 0.948 0.000 0.020 0.000 0.000 0.032
#> TCGA-06-0177-01A-01 1 0.6387 0.1658 0.476 0.000 0.308 0.000 0.180 0.036
#> TCGA-06-0238-01A-02 4 0.0806 0.8669 0.000 0.000 0.000 0.972 0.008 0.020
#> TCGA-06-0241-01A-02 1 0.4237 0.6673 0.736 0.000 0.144 0.000 0.000 0.120
#> TCGA-06-0410-01A-01 4 0.1765 0.8284 0.096 0.000 0.000 0.904 0.000 0.000
#> TCGA-06-0413-01A-01 1 0.0260 0.8694 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.3066 0.7647 0.832 0.000 0.124 0.000 0.000 0.044
#> TCGA-06-0646-01A-01 3 0.5197 0.6966 0.036 0.104 0.676 0.000 0.000 0.184
#> TCGA-06-0648-01A-01 5 0.5310 0.7083 0.192 0.000 0.048 0.004 0.676 0.080
#> TCGA-08-0245-01A-01 1 0.1261 0.8569 0.952 0.000 0.024 0.000 0.000 0.024
#> TCGA-08-0344-01A-01 1 0.1268 0.8528 0.952 0.000 0.036 0.000 0.008 0.004
#> TCGA-08-0347-01A-01 3 0.3275 0.7093 0.004 0.144 0.816 0.000 0.000 0.036
#> TCGA-08-0348-01A-01 3 0.5375 0.5707 0.268 0.008 0.596 0.000 0.000 0.128
#> TCGA-08-0350-01A-01 5 0.5413 0.7329 0.156 0.000 0.076 0.000 0.676 0.092
#> TCGA-08-0353-01A-01 3 0.4165 0.4084 0.420 0.008 0.568 0.000 0.000 0.004
#> TCGA-08-0359-01A-01 3 0.4894 0.6687 0.108 0.008 0.712 0.000 0.016 0.156
#> TCGA-08-0385-01A-01 5 0.5562 0.6729 0.224 0.000 0.044 0.008 0.644 0.080
#> TCGA-08-0517-01A-01 1 0.3351 0.4944 0.712 0.000 0.288 0.000 0.000 0.000
#> TCGA-08-0524-01A-01 1 0.0260 0.8694 0.992 0.000 0.008 0.000 0.000 0.000
#> TCGA-12-0616-01A-01 4 0.1524 0.8471 0.060 0.000 0.000 0.932 0.000 0.008
#> TCGA-12-0618-01A-01 1 0.1268 0.8528 0.952 0.000 0.036 0.000 0.008 0.004
#> TCGA-02-0089-01A-01 6 0.4651 0.4170 0.000 0.476 0.040 0.000 0.000 0.484
#> TCGA-02-0113-01A-01 3 0.3883 0.6457 0.000 0.088 0.768 0.000 0.000 0.144
#> TCGA-02-0115-01A-01 2 0.5877 0.1444 0.000 0.456 0.212 0.000 0.000 0.332
#> TCGA-02-0451-01A-01 2 0.6253 0.3736 0.040 0.536 0.204 0.000 0.000 0.220
#> TCGA-06-0132-01A-02 6 0.3168 0.6857 0.000 0.116 0.000 0.056 0.000 0.828
#> TCGA-06-0133-01A-02 4 0.0000 0.8748 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0138-01A-02 4 0.0146 0.8740 0.000 0.000 0.000 0.996 0.000 0.004
#> TCGA-06-0160-01A-01 4 0.6151 0.1525 0.024 0.000 0.028 0.512 0.356 0.080
#> TCGA-06-0162-01A-01 4 0.0000 0.8748 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0167-01A-01 4 0.4975 0.5648 0.016 0.000 0.008 0.684 0.216 0.076
#> TCGA-06-0171-01A-02 4 0.0713 0.8657 0.000 0.000 0.000 0.972 0.000 0.028
#> TCGA-06-0173-01A-01 3 0.4499 0.6580 0.108 0.008 0.724 0.000 0.000 0.160
#> TCGA-06-0179-01A-02 4 0.2048 0.8067 0.000 0.000 0.000 0.880 0.000 0.120
#> TCGA-06-0182-01A-01 4 0.0000 0.8748 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0185-01A-01 4 0.3888 0.6772 0.000 0.012 0.200 0.756 0.000 0.032
#> TCGA-06-0195-01B-01 4 0.1765 0.8284 0.096 0.000 0.000 0.904 0.000 0.000
#> TCGA-06-0208-01B-01 4 0.0000 0.8748 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0214-01A-02 3 0.5220 0.6501 0.048 0.084 0.676 0.000 0.000 0.192
#> TCGA-06-0219-01A-01 4 0.0000 0.8748 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0221-01A-01 4 0.0000 0.8748 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0237-01A-02 4 0.0000 0.8748 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-06-0240-01A-02 4 0.0000 0.8748 0.000 0.000 0.000 1.000 0.000 0.000
#> TCGA-08-0349-01A-01 3 0.5281 0.6378 0.040 0.052 0.608 0.000 0.000 0.300
#> TCGA-08-0380-01A-01 6 0.3457 0.7352 0.000 0.164 0.016 0.020 0.000 0.800
#> TCGA-08-0386-01A-01 3 0.3558 0.6470 0.248 0.016 0.736 0.000 0.000 0.000
#> TCGA-08-0520-01A-01 4 0.3691 0.7134 0.000 0.000 0.168 0.780 0.004 0.048
#> TCGA-02-0007-01A-01 3 0.3445 0.6499 0.244 0.012 0.744 0.000 0.000 0.000
#> TCGA-02-0009-01A-01 3 0.4890 0.4124 0.368 0.044 0.576 0.000 0.000 0.012
#> TCGA-02-0016-01A-01 3 0.4752 0.4283 0.020 0.012 0.672 0.000 0.268 0.028
#> TCGA-02-0021-01A-01 3 0.2748 0.7280 0.024 0.128 0.848 0.000 0.000 0.000
#> TCGA-02-0023-01B-01 5 0.3041 0.7766 0.000 0.000 0.128 0.000 0.832 0.040
#> TCGA-02-0027-01A-01 3 0.3073 0.7225 0.016 0.152 0.824 0.000 0.000 0.008
#> TCGA-02-0038-01A-01 2 0.4807 0.0595 0.000 0.484 0.464 0.000 0.000 0.052
#> TCGA-02-0043-01A-01 3 0.5414 0.2125 0.428 0.072 0.484 0.000 0.000 0.016
#> TCGA-02-0070-01A-01 3 0.3183 0.6936 0.008 0.200 0.788 0.000 0.000 0.004
#> TCGA-02-0102-01A-01 3 0.3246 0.7144 0.012 0.160 0.812 0.000 0.000 0.016
#> TCGA-02-0260-01A-03 5 0.1802 0.7901 0.000 0.000 0.012 0.000 0.916 0.072
#> TCGA-02-0269-01B-01 5 0.0405 0.7970 0.000 0.000 0.004 0.000 0.988 0.008
#> TCGA-02-0285-01A-01 3 0.4493 0.4817 0.000 0.312 0.636 0.000 0.000 0.052
#> TCGA-02-0289-01A-01 5 0.0146 0.7965 0.000 0.000 0.004 0.000 0.996 0.000
#> TCGA-02-0290-01A-01 5 0.4773 0.4118 0.000 0.004 0.048 0.000 0.572 0.376
#> TCGA-02-0317-01A-01 5 0.0000 0.7961 0.000 0.000 0.000 0.000 1.000 0.000
#> TCGA-02-0333-01A-02 5 0.0146 0.7965 0.000 0.000 0.004 0.000 0.996 0.000
#> TCGA-02-0422-01A-01 3 0.3248 0.6953 0.000 0.164 0.804 0.000 0.000 0.032
#> TCGA-02-0430-01A-01 3 0.3013 0.7151 0.140 0.024 0.832 0.000 0.000 0.004
#> TCGA-06-0125-01A-01 1 0.5208 -0.0817 0.488 0.060 0.440 0.000 0.000 0.012
#> TCGA-06-0126-01A-01 3 0.5387 0.5455 0.272 0.108 0.604 0.000 0.000 0.016
#> TCGA-06-0137-01A-03 3 0.3220 0.7271 0.032 0.112 0.840 0.000 0.012 0.004
#> TCGA-06-0145-01A-04 3 0.4057 0.4076 0.000 0.388 0.600 0.000 0.000 0.012
#> TCGA-06-0148-01A-01 5 0.3101 0.6886 0.000 0.032 0.148 0.000 0.820 0.000
#> TCGA-06-0187-01A-01 2 0.3975 0.0714 0.000 0.544 0.452 0.000 0.000 0.004
#> TCGA-06-0211-01B-01 3 0.3836 0.6517 0.252 0.012 0.724 0.000 0.000 0.012
#> TCGA-06-0402-01A-01 3 0.3375 0.7095 0.156 0.024 0.808 0.000 0.000 0.012
#> TCGA-08-0246-01A-01 2 0.3655 0.6898 0.000 0.788 0.136 0.000 0.000 0.076
#> TCGA-08-0354-01A-01 4 0.6272 0.3588 0.000 0.032 0.148 0.504 0.004 0.312
#> TCGA-08-0355-01A-01 5 0.3583 0.7655 0.000 0.008 0.144 0.000 0.800 0.048
#> TCGA-08-0357-01A-01 3 0.3120 0.7243 0.008 0.112 0.840 0.000 0.000 0.040
#> TCGA-08-0358-01A-01 5 0.0603 0.7962 0.000 0.000 0.004 0.000 0.980 0.016
#> TCGA-08-0375-01A-01 3 0.3463 0.6540 0.204 0.004 0.776 0.000 0.008 0.008
#> TCGA-08-0511-01A-01 3 0.2823 0.6853 0.000 0.204 0.796 0.000 0.000 0.000
#> TCGA-08-0514-01A-01 3 0.4228 0.3366 0.000 0.392 0.588 0.000 0.000 0.020
#> TCGA-08-0518-01A-01 3 0.3128 0.7103 0.008 0.168 0.812 0.000 0.000 0.012
#> TCGA-08-0529-01A-02 3 0.2737 0.7128 0.004 0.160 0.832 0.000 0.000 0.004
#> TCGA-08-0531-01A-01 3 0.2571 0.7169 0.000 0.064 0.876 0.000 0.000 0.060
#> TCGA-02-0057-01A-01 2 0.1588 0.7530 0.000 0.924 0.072 0.000 0.000 0.004
#> TCGA-02-0004-01A-01 6 0.3747 0.7466 0.000 0.396 0.000 0.000 0.000 0.604
#> TCGA-02-0006-01B-01 2 0.3435 0.6956 0.000 0.804 0.060 0.000 0.000 0.136
#> TCGA-02-0025-01A-01 6 0.4585 0.8081 0.000 0.284 0.000 0.000 0.068 0.648
#> TCGA-02-0033-01A-01 2 0.0717 0.7581 0.000 0.976 0.008 0.000 0.000 0.016
#> TCGA-02-0034-01A-01 2 0.0363 0.7583 0.000 0.988 0.012 0.000 0.000 0.000
#> TCGA-02-0039-01A-01 6 0.3890 0.7118 0.000 0.400 0.004 0.000 0.000 0.596
#> TCGA-02-0051-01A-01 6 0.4584 0.7658 0.000 0.184 0.064 0.000 0.028 0.724
#> TCGA-02-0054-01A-01 2 0.3268 0.6909 0.000 0.812 0.144 0.000 0.000 0.044
#> TCGA-02-0055-01A-01 6 0.3464 0.8568 0.000 0.312 0.000 0.000 0.000 0.688
#> TCGA-02-0059-01A-01 6 0.3309 0.8549 0.000 0.280 0.000 0.000 0.000 0.720
#> TCGA-02-0064-01A-01 2 0.0717 0.7547 0.000 0.976 0.016 0.000 0.000 0.008
#> TCGA-02-0075-01A-01 2 0.0717 0.7547 0.000 0.976 0.016 0.000 0.000 0.008
#> TCGA-02-0079-01A-03 5 0.5151 0.5496 0.000 0.008 0.092 0.000 0.604 0.296
#> TCGA-02-0085-01A-01 2 0.2499 0.7432 0.000 0.880 0.048 0.000 0.000 0.072
#> TCGA-02-0086-01A-01 2 0.4089 -0.4138 0.000 0.524 0.008 0.000 0.000 0.468
#> TCGA-02-0099-01A-01 2 0.3841 0.3094 0.000 0.616 0.380 0.000 0.000 0.004
#> TCGA-02-0106-01A-01 2 0.2006 0.7390 0.000 0.904 0.016 0.000 0.000 0.080
#> TCGA-02-0107-01A-01 6 0.3547 0.8415 0.000 0.332 0.000 0.000 0.000 0.668
#> TCGA-02-0111-01A-01 6 0.3409 0.8600 0.000 0.300 0.000 0.000 0.000 0.700
#> TCGA-02-0326-01A-01 5 0.0603 0.7962 0.000 0.000 0.004 0.000 0.980 0.016
#> TCGA-02-0337-01A-01 2 0.3158 0.7274 0.000 0.856 0.032 0.000 0.060 0.052
#> TCGA-06-0122-01A-01 2 0.2311 0.7076 0.000 0.880 0.104 0.000 0.000 0.016
#> TCGA-06-0124-01A-01 2 0.0717 0.7547 0.000 0.976 0.016 0.000 0.000 0.008
#> TCGA-06-0130-01A-01 2 0.1387 0.7356 0.000 0.932 0.000 0.000 0.000 0.068
#> TCGA-06-0139-01A-01 6 0.3464 0.8568 0.000 0.312 0.000 0.000 0.000 0.688
#> TCGA-06-0143-01A-01 2 0.3290 0.6257 0.000 0.776 0.208 0.000 0.000 0.016
#> TCGA-06-0147-01A-01 2 0.1866 0.7127 0.000 0.908 0.008 0.000 0.000 0.084
#> TCGA-06-0149-01A-05 2 0.4233 0.4161 0.000 0.684 0.048 0.000 0.000 0.268
#> TCGA-06-0152-01A-02 5 0.3617 0.7650 0.000 0.012 0.144 0.000 0.800 0.044
#> TCGA-06-0154-01A-02 2 0.0622 0.7626 0.000 0.980 0.008 0.000 0.000 0.012
#> TCGA-06-0164-01A-01 2 0.2312 0.7120 0.000 0.876 0.012 0.000 0.000 0.112
#> TCGA-06-0175-01A-01 2 0.4026 0.3847 0.000 0.636 0.348 0.000 0.000 0.016
#> TCGA-06-0176-01A-03 2 0.1391 0.7568 0.000 0.944 0.016 0.000 0.000 0.040
#> TCGA-06-0184-01A-01 6 0.3528 0.8600 0.000 0.296 0.004 0.000 0.000 0.700
#> TCGA-06-0189-01A-05 6 0.3351 0.8587 0.000 0.288 0.000 0.000 0.000 0.712
#> TCGA-06-0190-01A-01 2 0.1367 0.7555 0.000 0.944 0.012 0.000 0.000 0.044
#> TCGA-06-0194-01A-01 6 0.3499 0.8515 0.000 0.320 0.000 0.000 0.000 0.680
#> TCGA-06-0197-01A-02 6 0.3409 0.8601 0.000 0.300 0.000 0.000 0.000 0.700
#> TCGA-06-0210-01A-01 2 0.2815 0.7076 0.000 0.848 0.032 0.000 0.000 0.120
#> TCGA-06-0397-01A-01 2 0.0806 0.7644 0.000 0.972 0.020 0.000 0.000 0.008
#> TCGA-06-0409-01A-02 2 0.2697 0.5927 0.000 0.812 0.000 0.000 0.000 0.188
#> TCGA-06-0412-01A-01 2 0.1549 0.7558 0.000 0.936 0.020 0.000 0.000 0.044
#> TCGA-06-0644-01A-02 6 0.3578 0.8356 0.000 0.340 0.000 0.000 0.000 0.660
#> TCGA-06-0645-01A-01 2 0.3859 0.3574 0.000 0.692 0.020 0.000 0.000 0.288
#> TCGA-08-0346-01A-01 2 0.3081 0.5215 0.000 0.776 0.004 0.000 0.000 0.220
#> TCGA-08-0352-01A-01 2 0.2445 0.7033 0.000 0.872 0.108 0.000 0.000 0.020
#> TCGA-08-0360-01A-01 2 0.1814 0.7143 0.000 0.900 0.000 0.000 0.000 0.100
#> TCGA-08-0390-01A-01 6 0.3390 0.8602 0.000 0.296 0.000 0.000 0.000 0.704
#> TCGA-08-0392-01A-01 6 0.6698 0.5056 0.000 0.084 0.052 0.168 0.100 0.596
#> TCGA-08-0509-01A-01 2 0.0937 0.7552 0.000 0.960 0.000 0.000 0.000 0.040
#> TCGA-08-0510-01A-01 2 0.0603 0.7559 0.000 0.980 0.016 0.000 0.000 0.004
#> TCGA-08-0512-01A-01 2 0.0520 0.7592 0.000 0.984 0.008 0.000 0.000 0.008
#> TCGA-08-0522-01A-01 2 0.0363 0.7583 0.000 0.988 0.012 0.000 0.000 0.000
#> TCGA-12-0619-01A-01 2 0.1682 0.7605 0.000 0.928 0.052 0.000 0.000 0.020
#> TCGA-12-0620-01A-01 6 0.4788 0.7962 0.000 0.224 0.064 0.000 0.024 0.688
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> ATC:mclust 169 4.46e-19 2
#> ATC:mclust 130 1.36e-20 3
#> ATC:mclust 167 4.43e-28 4
#> ATC:mclust 117 2.20e-33 5
#> ATC:mclust 145 2.19e-43 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "NMF"]
# you can also extract it by
# res = res_list["ATC:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11268 rows and 173 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.964 0.951 0.980 0.5000 0.499 0.499
#> 3 3 0.659 0.817 0.890 0.2753 0.784 0.601
#> 4 4 0.540 0.535 0.770 0.1364 0.896 0.727
#> 5 5 0.655 0.673 0.812 0.0776 0.841 0.523
#> 6 6 0.716 0.632 0.787 0.0331 0.946 0.769
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA-02-0003-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0010-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0011-01B-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0014-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0024-01B-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0026-01B-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0028-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0046-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0047-01A-01 2 0.821 0.6475 0.256 0.744
#> TCGA-02-0048-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0060-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0069-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0074-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0080-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0084-01A-03 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0087-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0104-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0114-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0281-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0321-01A-01 1 0.416 0.9001 0.916 0.084
#> TCGA-02-0325-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0338-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0339-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0432-01A-02 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0439-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0440-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0446-01A-01 1 0.999 0.0868 0.520 0.480
#> TCGA-06-0128-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0129-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0146-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0156-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0166-01A-01 1 0.506 0.8705 0.888 0.112
#> TCGA-06-0174-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0177-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0238-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0241-01A-02 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0410-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0413-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0414-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0646-01A-01 2 0.952 0.3941 0.372 0.628
#> TCGA-06-0648-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0245-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0344-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0347-01A-01 1 0.260 0.9369 0.956 0.044
#> TCGA-08-0348-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0350-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0353-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0359-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0385-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0517-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0524-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-12-0616-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-12-0618-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0089-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0113-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0115-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0451-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0132-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0133-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0138-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0160-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0162-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0167-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0171-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0173-01A-01 2 0.981 0.2564 0.420 0.580
#> TCGA-06-0179-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0182-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0185-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0195-01B-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0208-01B-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0214-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0219-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0221-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0237-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0240-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0349-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0380-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0386-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0520-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0007-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0009-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0016-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0021-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0023-01B-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0027-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0038-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0043-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0070-01A-01 1 0.541 0.8569 0.876 0.124
#> TCGA-02-0102-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0260-01A-03 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0269-01B-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0285-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0289-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0290-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0317-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0333-01A-02 1 0.000 0.9734 1.000 0.000
#> TCGA-02-0422-01A-01 2 0.827 0.6406 0.260 0.740
#> TCGA-02-0430-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0125-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0126-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0137-01A-03 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0145-01A-04 1 0.900 0.5475 0.684 0.316
#> TCGA-06-0148-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0187-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0211-01B-01 1 0.000 0.9734 1.000 0.000
#> TCGA-06-0402-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0246-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0354-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0355-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0357-01A-01 1 0.388 0.9078 0.924 0.076
#> TCGA-08-0358-01A-01 1 0.844 0.6416 0.728 0.272
#> TCGA-08-0375-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0511-01A-01 1 0.456 0.8878 0.904 0.096
#> TCGA-08-0514-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0518-01A-01 1 0.000 0.9734 1.000 0.000
#> TCGA-08-0529-01A-02 1 0.714 0.7635 0.804 0.196
#> TCGA-08-0531-01A-01 1 0.861 0.6202 0.716 0.284
#> TCGA-02-0057-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0004-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0006-01B-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0025-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0033-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0034-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0039-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0051-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0054-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0055-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0059-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0064-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0075-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0079-01A-03 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0085-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0086-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0099-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0106-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0107-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0111-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0326-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-02-0337-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0122-01A-01 2 0.224 0.9483 0.036 0.964
#> TCGA-06-0124-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0130-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0139-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0143-01A-01 2 0.518 0.8582 0.116 0.884
#> TCGA-06-0147-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0149-01A-05 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0152-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0154-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0164-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0175-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0176-01A-03 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0184-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0189-01A-05 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0190-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0194-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0197-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0210-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0397-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0409-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0412-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0644-01A-02 2 0.000 0.9833 0.000 1.000
#> TCGA-06-0645-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0346-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0352-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0360-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0390-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0392-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0509-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0510-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0512-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-08-0522-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-12-0619-01A-01 2 0.000 0.9833 0.000 1.000
#> TCGA-12-0620-01A-01 2 0.000 0.9833 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA-02-0003-01A-01 1 0.0592 0.9184 0.988 0.000 0.012
#> TCGA-02-0010-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-02-0011-01B-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-02-0014-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-02-0024-01B-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-02-0026-01B-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-02-0028-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-02-0046-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-02-0047-01A-01 1 0.6451 0.5565 0.684 0.024 0.292
#> TCGA-02-0048-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-02-0060-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-02-0069-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-02-0074-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-02-0080-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-02-0084-01A-03 2 0.3851 0.8646 0.004 0.860 0.136
#> TCGA-02-0087-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-02-0104-01A-01 1 0.6286 0.0649 0.536 0.000 0.464
#> TCGA-02-0114-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-02-0281-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-02-0321-01A-01 1 0.0592 0.9189 0.988 0.000 0.012
#> TCGA-02-0325-01A-01 1 0.1129 0.9157 0.976 0.020 0.004
#> TCGA-02-0338-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-02-0339-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-02-0432-01A-02 1 0.0424 0.9199 0.992 0.000 0.008
#> TCGA-02-0439-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-02-0440-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-02-0446-01A-01 1 0.5191 0.7683 0.828 0.060 0.112
#> TCGA-06-0128-01A-01 3 0.6026 0.4138 0.376 0.000 0.624
#> TCGA-06-0129-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-06-0146-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-06-0156-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-06-0166-01A-01 1 0.2261 0.8811 0.932 0.000 0.068
#> TCGA-06-0174-01A-01 1 0.0592 0.9184 0.988 0.000 0.012
#> TCGA-06-0177-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-06-0238-01A-02 3 0.1129 0.8383 0.020 0.004 0.976
#> TCGA-06-0241-01A-02 1 0.4796 0.6970 0.780 0.000 0.220
#> TCGA-06-0410-01A-01 3 0.4654 0.6995 0.208 0.000 0.792
#> TCGA-06-0413-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-06-0414-01A-01 1 0.2448 0.8742 0.924 0.000 0.076
#> TCGA-06-0646-01A-01 1 0.5339 0.7655 0.824 0.080 0.096
#> TCGA-06-0648-01A-01 1 0.1289 0.9073 0.968 0.000 0.032
#> TCGA-08-0245-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-08-0344-01A-01 1 0.0747 0.9163 0.984 0.000 0.016
#> TCGA-08-0347-01A-01 1 0.0424 0.9204 0.992 0.008 0.000
#> TCGA-08-0348-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-08-0350-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-08-0353-01A-01 1 0.0000 0.9216 1.000 0.000 0.000
#> TCGA-08-0359-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-08-0385-01A-01 1 0.1289 0.9072 0.968 0.000 0.032
#> TCGA-08-0517-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-08-0524-01A-01 1 0.0237 0.9213 0.996 0.000 0.004
#> TCGA-12-0616-01A-01 3 0.4504 0.7120 0.196 0.000 0.804
#> TCGA-12-0618-01A-01 1 0.0424 0.9199 0.992 0.000 0.008
#> TCGA-02-0089-01A-01 2 0.5733 0.7015 0.000 0.676 0.324
#> TCGA-02-0113-01A-01 3 0.4121 0.6980 0.000 0.168 0.832
#> TCGA-02-0115-01A-01 3 0.4796 0.6086 0.000 0.220 0.780
#> TCGA-02-0451-01A-01 2 0.5810 0.6801 0.000 0.664 0.336
#> TCGA-06-0132-01A-02 3 0.1860 0.8220 0.000 0.052 0.948
#> TCGA-06-0133-01A-02 3 0.0237 0.8463 0.000 0.004 0.996
#> TCGA-06-0138-01A-02 3 0.0237 0.8463 0.000 0.004 0.996
#> TCGA-06-0160-01A-01 3 0.5621 0.5557 0.308 0.000 0.692
#> TCGA-06-0162-01A-01 3 0.1163 0.8372 0.000 0.028 0.972
#> TCGA-06-0167-01A-01 3 0.5058 0.6556 0.244 0.000 0.756
#> TCGA-06-0171-01A-02 3 0.0237 0.8463 0.000 0.004 0.996
#> TCGA-06-0173-01A-01 1 0.3377 0.8606 0.896 0.012 0.092
#> TCGA-06-0179-01A-02 3 0.0592 0.8440 0.000 0.012 0.988
#> TCGA-06-0182-01A-01 3 0.0237 0.8463 0.000 0.004 0.996
#> TCGA-06-0185-01A-01 3 0.0424 0.8456 0.000 0.008 0.992
#> TCGA-06-0195-01B-01 3 0.4291 0.7275 0.180 0.000 0.820
#> TCGA-06-0208-01B-01 3 0.0237 0.8463 0.000 0.004 0.996
#> TCGA-06-0214-01A-02 3 0.2711 0.7925 0.000 0.088 0.912
#> TCGA-06-0219-01A-01 3 0.0237 0.8463 0.000 0.004 0.996
#> TCGA-06-0221-01A-01 3 0.0237 0.8463 0.000 0.004 0.996
#> TCGA-06-0237-01A-02 3 0.0661 0.8436 0.008 0.004 0.988
#> TCGA-06-0240-01A-02 3 0.0237 0.8463 0.000 0.004 0.996
#> TCGA-08-0349-01A-01 3 0.0592 0.8445 0.000 0.012 0.988
#> TCGA-08-0380-01A-01 3 0.4346 0.6709 0.000 0.184 0.816
#> TCGA-08-0386-01A-01 1 0.1989 0.9047 0.948 0.048 0.004
#> TCGA-08-0520-01A-01 3 0.1289 0.8355 0.000 0.032 0.968
#> TCGA-02-0007-01A-01 1 0.3573 0.8639 0.876 0.120 0.004
#> TCGA-02-0009-01A-01 1 0.4351 0.8287 0.828 0.168 0.004
#> TCGA-02-0016-01A-01 1 0.3500 0.8667 0.880 0.116 0.004
#> TCGA-02-0021-01A-01 1 0.4465 0.8216 0.820 0.176 0.004
#> TCGA-02-0023-01B-01 2 0.4842 0.8062 0.000 0.776 0.224
#> TCGA-02-0027-01A-01 1 0.2301 0.8980 0.936 0.060 0.004
#> TCGA-02-0038-01A-01 2 0.4062 0.8581 0.000 0.836 0.164
#> TCGA-02-0043-01A-01 1 0.4465 0.8216 0.820 0.176 0.004
#> TCGA-02-0070-01A-01 2 0.4409 0.6385 0.172 0.824 0.004
#> TCGA-02-0102-01A-01 1 0.4575 0.8136 0.812 0.184 0.004
#> TCGA-02-0260-01A-03 1 0.0424 0.9203 0.992 0.008 0.000
#> TCGA-02-0269-01B-01 1 0.1765 0.9085 0.956 0.040 0.004
#> TCGA-02-0285-01A-01 2 0.0661 0.8265 0.008 0.988 0.004
#> TCGA-02-0289-01A-01 1 0.4409 0.8255 0.824 0.172 0.004
#> TCGA-02-0290-01A-01 2 0.6192 0.4947 0.000 0.580 0.420
#> TCGA-02-0317-01A-01 1 0.3644 0.8614 0.872 0.124 0.004
#> TCGA-02-0333-01A-02 1 0.4409 0.8255 0.824 0.172 0.004
#> TCGA-02-0422-01A-01 2 0.4834 0.5921 0.204 0.792 0.004
#> TCGA-02-0430-01A-01 1 0.2301 0.8991 0.936 0.060 0.004
#> TCGA-06-0125-01A-01 1 0.4409 0.8255 0.824 0.172 0.004
#> TCGA-06-0126-01A-01 1 0.3918 0.8505 0.856 0.140 0.004
#> TCGA-06-0137-01A-03 1 0.4351 0.8287 0.828 0.168 0.004
#> TCGA-06-0145-01A-04 2 0.3715 0.7006 0.128 0.868 0.004
#> TCGA-06-0148-01A-01 2 0.6209 0.2475 0.368 0.628 0.004
#> TCGA-06-0187-01A-01 2 0.0661 0.8265 0.008 0.988 0.004
#> TCGA-06-0211-01B-01 1 0.2711 0.8630 0.912 0.000 0.088
#> TCGA-06-0402-01A-01 1 0.4409 0.8253 0.824 0.172 0.004
#> TCGA-08-0246-01A-01 2 0.3686 0.8634 0.000 0.860 0.140
#> TCGA-08-0354-01A-01 3 0.2537 0.8009 0.000 0.080 0.920
#> TCGA-08-0355-01A-01 2 0.4062 0.8573 0.000 0.836 0.164
#> TCGA-08-0357-01A-01 1 0.2096 0.9033 0.944 0.052 0.004
#> TCGA-08-0358-01A-01 3 0.5431 0.6119 0.284 0.000 0.716
#> TCGA-08-0375-01A-01 1 0.0237 0.9210 0.996 0.004 0.000
#> TCGA-08-0511-01A-01 2 0.5588 0.4744 0.276 0.720 0.004
#> TCGA-08-0514-01A-01 2 0.0829 0.8235 0.012 0.984 0.004
#> TCGA-08-0518-01A-01 1 0.5201 0.7537 0.760 0.236 0.004
#> TCGA-08-0529-01A-02 1 0.6314 0.5090 0.604 0.392 0.004
#> TCGA-08-0531-01A-01 1 0.4465 0.8223 0.820 0.176 0.004
#> TCGA-02-0057-01A-01 2 0.0475 0.8346 0.004 0.992 0.004
#> TCGA-02-0004-01A-01 2 0.4235 0.8512 0.000 0.824 0.176
#> TCGA-02-0006-01B-01 2 0.4062 0.8567 0.000 0.836 0.164
#> TCGA-02-0025-01A-01 2 0.4121 0.8549 0.000 0.832 0.168
#> TCGA-02-0033-01A-01 2 0.2356 0.8594 0.000 0.928 0.072
#> TCGA-02-0034-01A-01 2 0.0747 0.8418 0.000 0.984 0.016
#> TCGA-02-0039-01A-01 2 0.3816 0.8608 0.000 0.852 0.148
#> TCGA-02-0051-01A-01 2 0.5016 0.8033 0.000 0.760 0.240
#> TCGA-02-0054-01A-01 2 0.1411 0.8494 0.000 0.964 0.036
#> TCGA-02-0055-01A-01 2 0.4702 0.8284 0.000 0.788 0.212
#> TCGA-02-0059-01A-01 2 0.5098 0.7954 0.000 0.752 0.248
#> TCGA-02-0064-01A-01 2 0.0237 0.8315 0.000 0.996 0.004
#> TCGA-02-0075-01A-01 2 0.0475 0.8292 0.004 0.992 0.004
#> TCGA-02-0079-01A-03 2 0.4235 0.8512 0.000 0.824 0.176
#> TCGA-02-0085-01A-01 2 0.4121 0.8550 0.000 0.832 0.168
#> TCGA-02-0086-01A-01 2 0.4346 0.8469 0.000 0.816 0.184
#> TCGA-02-0099-01A-01 2 0.0661 0.8369 0.004 0.988 0.008
#> TCGA-02-0106-01A-01 2 0.2537 0.8613 0.000 0.920 0.080
#> TCGA-02-0107-01A-01 2 0.4346 0.8469 0.000 0.816 0.184
#> TCGA-02-0111-01A-01 2 0.4555 0.8371 0.000 0.800 0.200
#> TCGA-02-0326-01A-01 2 0.4796 0.8237 0.000 0.780 0.220
#> TCGA-02-0337-01A-01 2 0.3752 0.8619 0.000 0.856 0.144
#> TCGA-06-0122-01A-01 2 0.1989 0.7923 0.048 0.948 0.004
#> TCGA-06-0124-01A-01 2 0.0475 0.8292 0.004 0.992 0.004
#> TCGA-06-0130-01A-01 2 0.3412 0.8642 0.000 0.876 0.124
#> TCGA-06-0139-01A-01 2 0.4654 0.8314 0.000 0.792 0.208
#> TCGA-06-0143-01A-01 2 0.2301 0.7805 0.060 0.936 0.004
#> TCGA-06-0147-01A-01 2 0.3116 0.8643 0.000 0.892 0.108
#> TCGA-06-0149-01A-05 2 0.3619 0.8634 0.000 0.864 0.136
#> TCGA-06-0152-01A-02 3 0.5859 0.3053 0.000 0.344 0.656
#> TCGA-06-0154-01A-02 2 0.0000 0.8341 0.000 1.000 0.000
#> TCGA-06-0164-01A-01 2 0.4002 0.8578 0.000 0.840 0.160
#> TCGA-06-0175-01A-01 2 0.0829 0.8389 0.004 0.984 0.012
#> TCGA-06-0176-01A-03 2 0.0747 0.8418 0.000 0.984 0.016
#> TCGA-06-0184-01A-01 2 0.4702 0.8283 0.000 0.788 0.212
#> TCGA-06-0189-01A-05 2 0.5098 0.7954 0.000 0.752 0.248
#> TCGA-06-0190-01A-01 2 0.3116 0.8643 0.000 0.892 0.108
#> TCGA-06-0194-01A-01 2 0.4399 0.8447 0.000 0.812 0.188
#> TCGA-06-0197-01A-02 2 0.5016 0.8033 0.000 0.760 0.240
#> TCGA-06-0210-01A-01 2 0.3941 0.8589 0.000 0.844 0.156
#> TCGA-06-0397-01A-01 2 0.0000 0.8341 0.000 1.000 0.000
#> TCGA-06-0409-01A-02 2 0.3619 0.8632 0.000 0.864 0.136
#> TCGA-06-0412-01A-01 2 0.2165 0.8576 0.000 0.936 0.064
#> TCGA-06-0644-01A-02 2 0.4235 0.8512 0.000 0.824 0.176
#> TCGA-06-0645-01A-01 2 0.4178 0.8533 0.000 0.828 0.172
#> TCGA-08-0346-01A-01 2 0.3116 0.8647 0.000 0.892 0.108
#> TCGA-08-0352-01A-01 2 0.0237 0.8315 0.000 0.996 0.004
#> TCGA-08-0360-01A-01 2 0.3038 0.8642 0.000 0.896 0.104
#> TCGA-08-0390-01A-01 2 0.5859 0.6591 0.000 0.656 0.344
#> TCGA-08-0392-01A-01 3 0.6302 -0.2182 0.000 0.480 0.520
#> TCGA-08-0509-01A-01 2 0.2711 0.8622 0.000 0.912 0.088
#> TCGA-08-0510-01A-01 2 0.0475 0.8292 0.004 0.992 0.004
#> TCGA-08-0512-01A-01 2 0.0592 0.8401 0.000 0.988 0.012
#> TCGA-08-0522-01A-01 2 0.0592 0.8401 0.000 0.988 0.012
#> TCGA-12-0619-01A-01 2 0.1411 0.8493 0.000 0.964 0.036
#> TCGA-12-0620-01A-01 2 0.4399 0.8447 0.000 0.812 0.188
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA-02-0003-01A-01 1 0.3931 0.6032 0.832 0.000 0.040 0.128
#> TCGA-02-0010-01A-01 1 0.0707 0.6565 0.980 0.000 0.020 0.000
#> TCGA-02-0011-01B-01 1 0.2125 0.6328 0.920 0.000 0.076 0.004
#> TCGA-02-0014-01A-01 1 0.0000 0.6573 1.000 0.000 0.000 0.000
#> TCGA-02-0024-01B-01 1 0.0817 0.6561 0.976 0.000 0.024 0.000
#> TCGA-02-0026-01B-01 1 0.1022 0.6542 0.968 0.000 0.032 0.000
#> TCGA-02-0028-01A-01 1 0.0707 0.6562 0.980 0.000 0.020 0.000
#> TCGA-02-0046-01A-01 1 0.1584 0.6476 0.952 0.000 0.036 0.012
#> TCGA-02-0047-01A-01 1 0.6578 0.2465 0.604 0.296 0.004 0.096
#> TCGA-02-0048-01A-01 1 0.3948 0.6106 0.840 0.000 0.064 0.096
#> TCGA-02-0060-01A-01 1 0.6299 0.2287 0.600 0.000 0.320 0.080
#> TCGA-02-0069-01A-01 1 0.0817 0.6556 0.976 0.000 0.024 0.000
#> TCGA-02-0074-01A-01 1 0.1211 0.6546 0.960 0.000 0.040 0.000
#> TCGA-02-0080-01A-01 1 0.5244 0.1046 0.556 0.000 0.436 0.008
#> TCGA-02-0084-01A-03 3 0.5981 0.3604 0.024 0.268 0.672 0.036
#> TCGA-02-0087-01A-01 3 0.6058 0.1593 0.424 0.004 0.536 0.036
#> TCGA-02-0104-01A-01 1 0.5838 0.1139 0.524 0.000 0.032 0.444
#> TCGA-02-0114-01A-01 1 0.3215 0.6215 0.876 0.000 0.032 0.092
#> TCGA-02-0281-01A-01 1 0.1211 0.6518 0.960 0.000 0.040 0.000
#> TCGA-02-0321-01A-01 1 0.7128 0.0650 0.496 0.016 0.404 0.084
#> TCGA-02-0325-01A-01 1 0.5257 0.0324 0.548 0.000 0.444 0.008
#> TCGA-02-0338-01A-01 1 0.0000 0.6573 1.000 0.000 0.000 0.000
#> TCGA-02-0339-01A-01 1 0.1302 0.6505 0.956 0.000 0.044 0.000
#> TCGA-02-0432-01A-02 1 0.5313 0.2431 0.608 0.000 0.376 0.016
#> TCGA-02-0439-01A-01 3 0.5755 0.1468 0.444 0.000 0.528 0.028
#> TCGA-02-0440-01A-01 1 0.1302 0.6505 0.956 0.000 0.000 0.044
#> TCGA-02-0446-01A-01 1 0.5911 0.2455 0.624 0.328 0.044 0.004
#> TCGA-06-0128-01A-01 4 0.5277 0.0356 0.460 0.000 0.008 0.532
#> TCGA-06-0129-01A-01 1 0.1118 0.6534 0.964 0.000 0.036 0.000
#> TCGA-06-0146-01A-01 1 0.3401 0.5702 0.840 0.000 0.152 0.008
#> TCGA-06-0156-01A-01 1 0.3831 0.6026 0.836 0.012 0.012 0.140
#> TCGA-06-0166-01A-01 1 0.5518 0.4991 0.708 0.016 0.032 0.244
#> TCGA-06-0174-01A-01 1 0.4224 0.5856 0.812 0.000 0.044 0.144
#> TCGA-06-0177-01A-01 1 0.1389 0.6501 0.952 0.000 0.048 0.000
#> TCGA-06-0238-01A-02 4 0.4331 0.7097 0.004 0.028 0.168 0.800
#> TCGA-06-0241-01A-02 1 0.5300 0.4478 0.664 0.000 0.028 0.308
#> TCGA-06-0410-01A-01 4 0.5367 0.4334 0.304 0.000 0.032 0.664
#> TCGA-06-0413-01A-01 1 0.1022 0.6542 0.968 0.000 0.032 0.000
#> TCGA-06-0414-01A-01 1 0.4955 0.4921 0.708 0.000 0.024 0.268
#> TCGA-06-0646-01A-01 1 0.4991 0.1284 0.608 0.388 0.000 0.004
#> TCGA-06-0648-01A-01 1 0.5404 0.4030 0.700 0.000 0.248 0.052
#> TCGA-08-0245-01A-01 1 0.3638 0.6077 0.848 0.000 0.032 0.120
#> TCGA-08-0344-01A-01 1 0.1510 0.6579 0.956 0.000 0.028 0.016
#> TCGA-08-0347-01A-01 1 0.6073 0.3641 0.680 0.080 0.232 0.008
#> TCGA-08-0348-01A-01 1 0.1545 0.6530 0.952 0.000 0.040 0.008
#> TCGA-08-0350-01A-01 1 0.5698 0.2643 0.608 0.000 0.356 0.036
#> TCGA-08-0353-01A-01 1 0.2334 0.6213 0.908 0.000 0.088 0.004
#> TCGA-08-0359-01A-01 1 0.6566 0.2588 0.600 0.000 0.288 0.112
#> TCGA-08-0385-01A-01 1 0.4775 0.4479 0.740 0.000 0.232 0.028
#> TCGA-08-0517-01A-01 1 0.5334 0.5299 0.740 0.000 0.172 0.088
#> TCGA-08-0524-01A-01 1 0.0672 0.6571 0.984 0.000 0.008 0.008
#> TCGA-12-0616-01A-01 4 0.5564 0.1512 0.436 0.000 0.020 0.544
#> TCGA-12-0618-01A-01 1 0.1284 0.6579 0.964 0.000 0.024 0.012
#> TCGA-02-0089-01A-01 2 0.5256 0.3544 0.000 0.596 0.012 0.392
#> TCGA-02-0113-01A-01 4 0.7398 0.2207 0.008 0.360 0.136 0.496
#> TCGA-02-0115-01A-01 4 0.6111 0.2278 0.000 0.392 0.052 0.556
#> TCGA-02-0451-01A-01 2 0.4606 0.5964 0.000 0.724 0.012 0.264
#> TCGA-06-0132-01A-02 4 0.5369 0.6705 0.000 0.112 0.144 0.744
#> TCGA-06-0133-01A-02 4 0.1109 0.7769 0.000 0.028 0.004 0.968
#> TCGA-06-0138-01A-02 4 0.2483 0.7686 0.000 0.032 0.052 0.916
#> TCGA-06-0160-01A-01 4 0.5434 0.5763 0.132 0.000 0.128 0.740
#> TCGA-06-0162-01A-01 4 0.3732 0.7462 0.000 0.056 0.092 0.852
#> TCGA-06-0167-01A-01 4 0.3367 0.7090 0.028 0.000 0.108 0.864
#> TCGA-06-0171-01A-02 4 0.1510 0.7738 0.016 0.028 0.000 0.956
#> TCGA-06-0173-01A-01 1 0.8173 0.2845 0.520 0.068 0.116 0.296
#> TCGA-06-0179-01A-02 4 0.1305 0.7764 0.004 0.036 0.000 0.960
#> TCGA-06-0182-01A-01 4 0.2432 0.7604 0.020 0.028 0.024 0.928
#> TCGA-06-0185-01A-01 4 0.1004 0.7759 0.000 0.024 0.004 0.972
#> TCGA-06-0195-01B-01 4 0.2197 0.7255 0.080 0.000 0.004 0.916
#> TCGA-06-0208-01B-01 4 0.1762 0.7653 0.020 0.016 0.012 0.952
#> TCGA-06-0214-01A-02 4 0.5161 0.3314 0.000 0.400 0.008 0.592
#> TCGA-06-0219-01A-01 4 0.1256 0.7772 0.000 0.028 0.008 0.964
#> TCGA-06-0221-01A-01 4 0.1484 0.7752 0.004 0.020 0.016 0.960
#> TCGA-06-0237-01A-02 4 0.1284 0.7759 0.000 0.024 0.012 0.964
#> TCGA-06-0240-01A-02 4 0.1929 0.7728 0.000 0.024 0.036 0.940
#> TCGA-08-0349-01A-01 4 0.4905 0.7142 0.004 0.112 0.096 0.788
#> TCGA-08-0380-01A-01 4 0.6916 0.4752 0.000 0.280 0.148 0.572
#> TCGA-08-0386-01A-01 1 0.4647 0.3683 0.704 0.008 0.288 0.000
#> TCGA-08-0520-01A-01 4 0.2773 0.7610 0.000 0.028 0.072 0.900
#> TCGA-02-0007-01A-01 1 0.4722 0.3541 0.692 0.008 0.300 0.000
#> TCGA-02-0009-01A-01 3 0.5168 0.0954 0.496 0.004 0.500 0.000
#> TCGA-02-0016-01A-01 3 0.5294 0.1513 0.484 0.000 0.508 0.008
#> TCGA-02-0021-01A-01 1 0.5823 0.2335 0.608 0.044 0.348 0.000
#> TCGA-02-0023-01B-01 3 0.5159 0.3797 0.000 0.156 0.756 0.088
#> TCGA-02-0027-01A-01 1 0.4482 0.3874 0.728 0.000 0.264 0.008
#> TCGA-02-0038-01A-01 2 0.5672 0.6265 0.008 0.668 0.288 0.036
#> TCGA-02-0043-01A-01 1 0.5057 0.3107 0.648 0.012 0.340 0.000
#> TCGA-02-0070-01A-01 3 0.7084 0.4101 0.176 0.264 0.560 0.000
#> TCGA-02-0102-01A-01 3 0.5853 0.1432 0.460 0.032 0.508 0.000
#> TCGA-02-0260-01A-03 1 0.5168 -0.1007 0.500 0.000 0.496 0.004
#> TCGA-02-0269-01B-01 3 0.4955 0.3522 0.344 0.000 0.648 0.008
#> TCGA-02-0285-01A-01 2 0.5696 0.2677 0.024 0.496 0.480 0.000
#> TCGA-02-0289-01A-01 3 0.4899 0.3999 0.300 0.004 0.688 0.008
#> TCGA-02-0290-01A-01 3 0.7402 0.0954 0.000 0.264 0.516 0.220
#> TCGA-02-0317-01A-01 3 0.3972 0.4427 0.204 0.000 0.788 0.008
#> TCGA-02-0333-01A-02 3 0.4991 0.3808 0.316 0.004 0.672 0.008
#> TCGA-02-0422-01A-01 2 0.6990 0.2275 0.116 0.476 0.408 0.000
#> TCGA-02-0430-01A-01 1 0.4914 0.3522 0.676 0.012 0.312 0.000
#> TCGA-06-0125-01A-01 1 0.5165 -0.0949 0.512 0.004 0.484 0.000
#> TCGA-06-0126-01A-01 1 0.5080 0.0713 0.576 0.000 0.420 0.004
#> TCGA-06-0137-01A-03 3 0.5112 0.2094 0.436 0.004 0.560 0.000
#> TCGA-06-0145-01A-04 2 0.6213 0.2668 0.052 0.484 0.464 0.000
#> TCGA-06-0148-01A-01 3 0.5995 0.4543 0.232 0.096 0.672 0.000
#> TCGA-06-0187-01A-01 2 0.4825 0.6456 0.008 0.700 0.288 0.004
#> TCGA-06-0211-01B-01 1 0.7314 0.2754 0.496 0.000 0.168 0.336
#> TCGA-06-0402-01A-01 1 0.7008 0.2027 0.572 0.136 0.288 0.004
#> TCGA-08-0246-01A-01 2 0.4606 0.6742 0.000 0.724 0.264 0.012
#> TCGA-08-0354-01A-01 4 0.5951 0.6479 0.000 0.152 0.152 0.696
#> TCGA-08-0355-01A-01 3 0.5247 0.3859 0.000 0.228 0.720 0.052
#> TCGA-08-0357-01A-01 3 0.7010 0.2241 0.448 0.100 0.448 0.004
#> TCGA-08-0358-01A-01 3 0.7780 0.0814 0.232 0.004 0.464 0.300
#> TCGA-08-0375-01A-01 1 0.2814 0.5888 0.868 0.000 0.132 0.000
#> TCGA-08-0511-01A-01 2 0.6213 0.2722 0.052 0.484 0.464 0.000
#> TCGA-08-0514-01A-01 2 0.5085 0.5354 0.008 0.616 0.376 0.000
#> TCGA-08-0518-01A-01 3 0.6477 0.2732 0.368 0.080 0.552 0.000
#> TCGA-08-0529-01A-02 3 0.7479 0.3326 0.252 0.244 0.504 0.000
#> TCGA-08-0531-01A-01 3 0.7709 0.3157 0.276 0.132 0.556 0.036
#> TCGA-02-0057-01A-01 2 0.4948 0.5408 0.004 0.696 0.288 0.012
#> TCGA-02-0004-01A-01 2 0.0524 0.8060 0.000 0.988 0.008 0.004
#> TCGA-02-0006-01B-01 2 0.1938 0.8010 0.000 0.936 0.052 0.012
#> TCGA-02-0025-01A-01 2 0.3450 0.7088 0.000 0.836 0.156 0.008
#> TCGA-02-0033-01A-01 2 0.0817 0.8050 0.000 0.976 0.024 0.000
#> TCGA-02-0034-01A-01 2 0.0592 0.8050 0.000 0.984 0.016 0.000
#> TCGA-02-0039-01A-01 2 0.2198 0.7764 0.000 0.920 0.072 0.008
#> TCGA-02-0051-01A-01 2 0.0804 0.8060 0.000 0.980 0.008 0.012
#> TCGA-02-0054-01A-01 2 0.4114 0.7274 0.008 0.788 0.200 0.004
#> TCGA-02-0055-01A-01 2 0.0779 0.8029 0.000 0.980 0.004 0.016
#> TCGA-02-0059-01A-01 2 0.2256 0.7837 0.000 0.924 0.056 0.020
#> TCGA-02-0064-01A-01 2 0.1940 0.7979 0.000 0.924 0.076 0.000
#> TCGA-02-0075-01A-01 2 0.4539 0.6649 0.008 0.720 0.272 0.000
#> TCGA-02-0079-01A-03 2 0.5778 0.3664 0.000 0.604 0.356 0.040
#> TCGA-02-0085-01A-01 2 0.1798 0.7900 0.000 0.944 0.040 0.016
#> TCGA-02-0086-01A-01 2 0.2473 0.7943 0.000 0.908 0.080 0.012
#> TCGA-02-0099-01A-01 2 0.4192 0.7218 0.008 0.780 0.208 0.004
#> TCGA-02-0106-01A-01 2 0.3441 0.7595 0.004 0.840 0.152 0.004
#> TCGA-02-0107-01A-01 2 0.0927 0.8016 0.000 0.976 0.008 0.016
#> TCGA-02-0111-01A-01 2 0.2563 0.7715 0.000 0.908 0.072 0.020
#> TCGA-02-0326-01A-01 3 0.6780 0.2860 0.012 0.252 0.624 0.112
#> TCGA-02-0337-01A-01 2 0.5543 0.2628 0.000 0.556 0.424 0.020
#> TCGA-06-0122-01A-01 2 0.5590 0.3502 0.020 0.524 0.456 0.000
#> TCGA-06-0124-01A-01 2 0.3649 0.7340 0.000 0.796 0.204 0.000
#> TCGA-06-0130-01A-01 2 0.0188 0.8050 0.000 0.996 0.004 0.000
#> TCGA-06-0139-01A-01 2 0.1174 0.8002 0.000 0.968 0.012 0.020
#> TCGA-06-0143-01A-01 2 0.5150 0.6122 0.040 0.744 0.208 0.008
#> TCGA-06-0147-01A-01 2 0.0524 0.8031 0.000 0.988 0.008 0.004
#> TCGA-06-0149-01A-05 2 0.4980 0.5435 0.000 0.680 0.304 0.016
#> TCGA-06-0152-01A-02 3 0.7818 -0.1231 0.000 0.268 0.408 0.324
#> TCGA-06-0154-01A-02 2 0.1557 0.8011 0.000 0.944 0.056 0.000
#> TCGA-06-0164-01A-01 2 0.0895 0.8062 0.000 0.976 0.020 0.004
#> TCGA-06-0175-01A-01 2 0.4267 0.7148 0.008 0.772 0.216 0.004
#> TCGA-06-0176-01A-03 2 0.2714 0.7814 0.000 0.884 0.112 0.004
#> TCGA-06-0184-01A-01 2 0.1151 0.8004 0.000 0.968 0.008 0.024
#> TCGA-06-0189-01A-05 2 0.2021 0.7887 0.000 0.936 0.040 0.024
#> TCGA-06-0190-01A-01 2 0.0921 0.8056 0.000 0.972 0.028 0.000
#> TCGA-06-0194-01A-01 2 0.0779 0.8029 0.000 0.980 0.004 0.016
#> TCGA-06-0197-01A-02 2 0.1151 0.8005 0.000 0.968 0.008 0.024
#> TCGA-06-0210-01A-01 2 0.2676 0.7919 0.000 0.896 0.092 0.012
#> TCGA-06-0397-01A-01 2 0.3583 0.7437 0.004 0.816 0.180 0.000
#> TCGA-06-0409-01A-02 2 0.0672 0.8024 0.000 0.984 0.008 0.008
#> TCGA-06-0412-01A-01 2 0.3400 0.7449 0.000 0.820 0.180 0.000
#> TCGA-06-0644-01A-02 2 0.1004 0.8063 0.000 0.972 0.024 0.004
#> TCGA-06-0645-01A-01 2 0.1388 0.7960 0.000 0.960 0.028 0.012
#> TCGA-08-0346-01A-01 2 0.1978 0.7803 0.000 0.928 0.068 0.004
#> TCGA-08-0352-01A-01 2 0.4679 0.5251 0.000 0.648 0.352 0.000
#> TCGA-08-0360-01A-01 2 0.0524 0.8031 0.000 0.988 0.008 0.004
#> TCGA-08-0390-01A-01 2 0.2830 0.7713 0.000 0.900 0.040 0.060
#> TCGA-08-0392-01A-01 2 0.6098 0.5027 0.000 0.676 0.124 0.200
#> TCGA-08-0509-01A-01 2 0.0524 0.8032 0.000 0.988 0.004 0.008
#> TCGA-08-0510-01A-01 2 0.4401 0.6657 0.004 0.724 0.272 0.000
#> TCGA-08-0512-01A-01 2 0.0921 0.8045 0.000 0.972 0.028 0.000
#> TCGA-08-0522-01A-01 2 0.1022 0.8045 0.000 0.968 0.032 0.000
#> TCGA-12-0619-01A-01 2 0.0592 0.8052 0.000 0.984 0.016 0.000
#> TCGA-12-0620-01A-01 2 0.5113 0.5108 0.000 0.684 0.292 0.024
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA-02-0003-01A-01 1 0.2026 0.7835 0.924 0.000 0.008 0.012 0.056
#> TCGA-02-0010-01A-01 1 0.2124 0.7979 0.916 0.000 0.028 0.000 0.056
#> TCGA-02-0011-01B-01 1 0.3962 0.7221 0.800 0.000 0.088 0.000 0.112
#> TCGA-02-0014-01A-01 1 0.0609 0.8038 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0024-01B-01 1 0.2236 0.7959 0.908 0.000 0.024 0.000 0.068
#> TCGA-02-0026-01B-01 1 0.2450 0.7918 0.896 0.000 0.028 0.000 0.076
#> TCGA-02-0028-01A-01 1 0.1430 0.7889 0.944 0.000 0.004 0.000 0.052
#> TCGA-02-0046-01A-01 1 0.1117 0.8035 0.964 0.000 0.020 0.000 0.016
#> TCGA-02-0047-01A-01 1 0.7751 0.2851 0.512 0.196 0.020 0.204 0.068
#> TCGA-02-0048-01A-01 1 0.2243 0.7799 0.916 0.000 0.016 0.012 0.056
#> TCGA-02-0060-01A-01 5 0.6761 0.2219 0.396 0.000 0.136 0.024 0.444
#> TCGA-02-0069-01A-01 1 0.2124 0.7982 0.916 0.000 0.028 0.000 0.056
#> TCGA-02-0074-01A-01 1 0.1568 0.8033 0.944 0.000 0.036 0.000 0.020
#> TCGA-02-0080-01A-01 5 0.5870 0.5105 0.284 0.000 0.136 0.000 0.580
#> TCGA-02-0084-01A-03 5 0.5456 0.6259 0.052 0.068 0.168 0.000 0.712
#> TCGA-02-0087-01A-01 5 0.5508 0.6408 0.120 0.004 0.184 0.008 0.684
#> TCGA-02-0104-01A-01 1 0.4193 0.6966 0.808 0.000 0.024 0.100 0.068
#> TCGA-02-0114-01A-01 1 0.1571 0.7858 0.936 0.000 0.004 0.000 0.060
#> TCGA-02-0281-01A-01 1 0.2450 0.7918 0.896 0.000 0.028 0.000 0.076
#> TCGA-02-0321-01A-01 5 0.5639 0.1444 0.400 0.052 0.012 0.000 0.536
#> TCGA-02-0325-01A-01 5 0.6403 0.5728 0.232 0.000 0.256 0.000 0.512
#> TCGA-02-0338-01A-01 1 0.0609 0.8005 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0339-01A-01 1 0.3090 0.7721 0.860 0.000 0.052 0.000 0.088
#> TCGA-02-0432-01A-02 5 0.5965 0.4269 0.328 0.000 0.128 0.000 0.544
#> TCGA-02-0439-01A-01 5 0.5926 0.6189 0.116 0.000 0.260 0.012 0.612
#> TCGA-02-0440-01A-01 1 0.0404 0.8034 0.988 0.000 0.000 0.000 0.012
#> TCGA-02-0446-01A-01 1 0.4030 0.6125 0.772 0.200 0.008 0.004 0.016
#> TCGA-06-0128-01A-01 1 0.5256 0.4376 0.608 0.000 0.016 0.344 0.032
#> TCGA-06-0129-01A-01 1 0.3033 0.7762 0.864 0.000 0.052 0.000 0.084
#> TCGA-06-0146-01A-01 1 0.4203 0.7026 0.780 0.000 0.092 0.000 0.128
#> TCGA-06-0156-01A-01 1 0.1016 0.8036 0.972 0.004 0.004 0.012 0.008
#> TCGA-06-0166-01A-01 1 0.1924 0.7812 0.924 0.000 0.008 0.004 0.064
#> TCGA-06-0174-01A-01 1 0.1731 0.7847 0.932 0.000 0.004 0.004 0.060
#> TCGA-06-0177-01A-01 1 0.2754 0.7844 0.880 0.000 0.040 0.000 0.080
#> TCGA-06-0238-01A-02 4 0.4162 0.6016 0.004 0.000 0.004 0.680 0.312
#> TCGA-06-0241-01A-02 1 0.2419 0.7720 0.904 0.000 0.004 0.028 0.064
#> TCGA-06-0410-01A-01 4 0.5302 0.6137 0.212 0.000 0.024 0.696 0.068
#> TCGA-06-0413-01A-01 1 0.2388 0.7931 0.900 0.000 0.028 0.000 0.072
#> TCGA-06-0414-01A-01 1 0.2141 0.7776 0.916 0.000 0.004 0.016 0.064
#> TCGA-06-0646-01A-01 1 0.4682 0.3705 0.620 0.356 0.000 0.000 0.024
#> TCGA-06-0648-01A-01 1 0.5006 0.4963 0.644 0.000 0.044 0.004 0.308
#> TCGA-08-0245-01A-01 1 0.1638 0.7844 0.932 0.000 0.004 0.000 0.064
#> TCGA-08-0344-01A-01 1 0.2608 0.7912 0.888 0.000 0.020 0.004 0.088
#> TCGA-08-0347-01A-01 1 0.7017 0.3541 0.564 0.128 0.084 0.000 0.224
#> TCGA-08-0348-01A-01 1 0.3373 0.7665 0.848 0.000 0.056 0.004 0.092
#> TCGA-08-0350-01A-01 1 0.5176 0.0873 0.492 0.000 0.040 0.000 0.468
#> TCGA-08-0353-01A-01 1 0.2069 0.7672 0.912 0.000 0.076 0.000 0.012
#> TCGA-08-0359-01A-01 1 0.5704 0.5801 0.668 0.000 0.092 0.028 0.212
#> TCGA-08-0385-01A-01 1 0.4774 0.5564 0.680 0.000 0.040 0.004 0.276
#> TCGA-08-0517-01A-01 1 0.2141 0.7797 0.916 0.000 0.016 0.004 0.064
#> TCGA-08-0524-01A-01 1 0.0566 0.8038 0.984 0.000 0.004 0.000 0.012
#> TCGA-12-0616-01A-01 1 0.4684 0.6516 0.764 0.000 0.024 0.148 0.064
#> TCGA-12-0618-01A-01 1 0.2670 0.7906 0.888 0.000 0.028 0.004 0.080
#> TCGA-02-0089-01A-01 4 0.3046 0.7727 0.000 0.076 0.028 0.876 0.020
#> TCGA-02-0113-01A-01 4 0.5167 0.6390 0.000 0.036 0.204 0.712 0.048
#> TCGA-02-0115-01A-01 4 0.2916 0.7831 0.000 0.008 0.072 0.880 0.040
#> TCGA-02-0451-01A-01 4 0.4167 0.7056 0.000 0.160 0.028 0.788 0.024
#> TCGA-06-0132-01A-02 4 0.5549 0.6215 0.000 0.200 0.016 0.676 0.108
#> TCGA-06-0133-01A-02 4 0.0854 0.8115 0.000 0.004 0.012 0.976 0.008
#> TCGA-06-0138-01A-02 4 0.1026 0.8117 0.000 0.004 0.004 0.968 0.024
#> TCGA-06-0160-01A-01 4 0.6196 0.1366 0.088 0.000 0.016 0.480 0.416
#> TCGA-06-0162-01A-01 4 0.1908 0.8104 0.000 0.024 0.016 0.936 0.024
#> TCGA-06-0167-01A-01 4 0.5284 0.4632 0.036 0.000 0.016 0.616 0.332
#> TCGA-06-0171-01A-02 4 0.0324 0.8129 0.004 0.004 0.000 0.992 0.000
#> TCGA-06-0173-01A-01 4 0.7258 0.4049 0.296 0.036 0.084 0.536 0.048
#> TCGA-06-0179-01A-02 4 0.1074 0.8103 0.000 0.004 0.016 0.968 0.012
#> TCGA-06-0182-01A-01 4 0.2045 0.8070 0.012 0.004 0.020 0.932 0.032
#> TCGA-06-0185-01A-01 4 0.0807 0.8124 0.000 0.000 0.012 0.976 0.012
#> TCGA-06-0195-01B-01 4 0.0727 0.8105 0.004 0.000 0.012 0.980 0.004
#> TCGA-06-0208-01B-01 4 0.1026 0.8116 0.004 0.004 0.000 0.968 0.024
#> TCGA-06-0214-01A-02 4 0.2027 0.8051 0.000 0.040 0.008 0.928 0.024
#> TCGA-06-0219-01A-01 4 0.1059 0.8120 0.000 0.004 0.020 0.968 0.008
#> TCGA-06-0221-01A-01 4 0.1041 0.8107 0.000 0.000 0.004 0.964 0.032
#> TCGA-06-0237-01A-02 4 0.0404 0.8120 0.000 0.000 0.000 0.988 0.012
#> TCGA-06-0240-01A-02 4 0.1740 0.8015 0.000 0.000 0.012 0.932 0.056
#> TCGA-08-0349-01A-01 4 0.6484 0.6186 0.036 0.160 0.020 0.648 0.136
#> TCGA-08-0380-01A-01 4 0.5605 0.4579 0.000 0.332 0.016 0.596 0.056
#> TCGA-08-0386-01A-01 3 0.4577 0.6172 0.208 0.000 0.736 0.008 0.048
#> TCGA-08-0520-01A-01 4 0.1597 0.8108 0.000 0.008 0.020 0.948 0.024
#> TCGA-02-0007-01A-01 3 0.4147 0.6642 0.172 0.004 0.776 0.000 0.048
#> TCGA-02-0009-01A-01 3 0.2376 0.7140 0.052 0.000 0.904 0.000 0.044
#> TCGA-02-0016-01A-01 3 0.3650 0.5911 0.028 0.000 0.796 0.000 0.176
#> TCGA-02-0021-01A-01 3 0.2992 0.7250 0.092 0.012 0.872 0.000 0.024
#> TCGA-02-0023-01B-01 5 0.5558 0.4768 0.000 0.048 0.276 0.032 0.644
#> TCGA-02-0027-01A-01 1 0.6685 -0.2827 0.384 0.000 0.380 0.000 0.236
#> TCGA-02-0038-01A-01 3 0.5862 0.6059 0.000 0.144 0.684 0.124 0.048
#> TCGA-02-0043-01A-01 3 0.3300 0.6176 0.204 0.000 0.792 0.000 0.004
#> TCGA-02-0070-01A-01 3 0.4055 0.6606 0.012 0.048 0.800 0.000 0.140
#> TCGA-02-0102-01A-01 3 0.2433 0.7305 0.056 0.012 0.908 0.000 0.024
#> TCGA-02-0260-01A-03 5 0.6401 0.5490 0.184 0.000 0.336 0.000 0.480
#> TCGA-02-0269-01B-01 5 0.5571 0.5451 0.084 0.000 0.348 0.000 0.568
#> TCGA-02-0285-01A-01 3 0.4269 0.6937 0.000 0.116 0.776 0.000 0.108
#> TCGA-02-0289-01A-01 3 0.4654 0.1801 0.024 0.000 0.628 0.000 0.348
#> TCGA-02-0290-01A-01 5 0.7991 -0.0802 0.000 0.084 0.248 0.324 0.344
#> TCGA-02-0317-01A-01 5 0.4682 0.4551 0.024 0.000 0.356 0.000 0.620
#> TCGA-02-0333-01A-02 5 0.4980 0.4860 0.036 0.000 0.380 0.000 0.584
#> TCGA-02-0422-01A-01 3 0.2995 0.7410 0.032 0.088 0.872 0.000 0.008
#> TCGA-02-0430-01A-01 3 0.3693 0.6890 0.156 0.004 0.808 0.000 0.032
#> TCGA-06-0125-01A-01 3 0.2278 0.7200 0.060 0.000 0.908 0.000 0.032
#> TCGA-06-0126-01A-01 3 0.4845 0.5201 0.128 0.000 0.724 0.000 0.148
#> TCGA-06-0137-01A-03 3 0.3532 0.6415 0.048 0.000 0.824 0.000 0.128
#> TCGA-06-0145-01A-04 3 0.3909 0.7237 0.004 0.124 0.808 0.000 0.064
#> TCGA-06-0148-01A-01 3 0.3053 0.6189 0.008 0.000 0.828 0.000 0.164
#> TCGA-06-0187-01A-01 3 0.3927 0.6839 0.000 0.164 0.792 0.004 0.040
#> TCGA-06-0211-01B-01 4 0.6694 0.4604 0.136 0.000 0.240 0.576 0.048
#> TCGA-06-0402-01A-01 3 0.4763 0.6469 0.180 0.012 0.752 0.012 0.044
#> TCGA-08-0246-01A-01 3 0.2763 0.7093 0.000 0.148 0.848 0.004 0.000
#> TCGA-08-0354-01A-01 4 0.5357 0.6550 0.000 0.068 0.020 0.680 0.232
#> TCGA-08-0355-01A-01 5 0.5360 0.3091 0.000 0.060 0.384 0.000 0.556
#> TCGA-08-0357-01A-01 3 0.2538 0.7152 0.048 0.004 0.900 0.000 0.048
#> TCGA-08-0358-01A-01 5 0.5040 0.5543 0.072 0.028 0.036 0.084 0.780
#> TCGA-08-0375-01A-01 3 0.5856 0.0182 0.396 0.000 0.504 0.000 0.100
#> TCGA-08-0511-01A-01 3 0.3056 0.7341 0.008 0.112 0.860 0.000 0.020
#> TCGA-08-0514-01A-01 3 0.2818 0.7199 0.000 0.128 0.860 0.004 0.008
#> TCGA-08-0518-01A-01 3 0.2418 0.7379 0.044 0.024 0.912 0.000 0.020
#> TCGA-08-0529-01A-02 3 0.2618 0.7464 0.036 0.052 0.900 0.000 0.012
#> TCGA-08-0531-01A-01 3 0.3270 0.7295 0.032 0.020 0.876 0.060 0.012
#> TCGA-02-0057-01A-01 3 0.6525 0.3625 0.000 0.224 0.512 0.004 0.260
#> TCGA-02-0004-01A-01 2 0.0798 0.8723 0.000 0.976 0.008 0.000 0.016
#> TCGA-02-0006-01B-01 2 0.1862 0.8578 0.000 0.932 0.048 0.004 0.016
#> TCGA-02-0025-01A-01 2 0.2488 0.8015 0.000 0.872 0.000 0.004 0.124
#> TCGA-02-0033-01A-01 2 0.0290 0.8735 0.000 0.992 0.008 0.000 0.000
#> TCGA-02-0034-01A-01 2 0.0609 0.8716 0.000 0.980 0.000 0.000 0.020
#> TCGA-02-0039-01A-01 2 0.0510 0.8731 0.000 0.984 0.000 0.000 0.016
#> TCGA-02-0051-01A-01 2 0.2591 0.8445 0.000 0.904 0.032 0.020 0.044
#> TCGA-02-0054-01A-01 2 0.4691 0.4839 0.000 0.636 0.340 0.004 0.020
#> TCGA-02-0055-01A-01 2 0.0798 0.8727 0.000 0.976 0.008 0.000 0.016
#> TCGA-02-0059-01A-01 2 0.2988 0.8156 0.000 0.880 0.024 0.024 0.072
#> TCGA-02-0064-01A-01 2 0.2964 0.8008 0.000 0.856 0.120 0.000 0.024
#> TCGA-02-0075-01A-01 3 0.4497 0.2285 0.000 0.424 0.568 0.000 0.008
#> TCGA-02-0079-01A-03 2 0.4414 0.4457 0.000 0.616 0.004 0.004 0.376
#> TCGA-02-0085-01A-01 2 0.1041 0.8693 0.000 0.964 0.004 0.000 0.032
#> TCGA-02-0086-01A-01 2 0.3174 0.7974 0.000 0.844 0.132 0.004 0.020
#> TCGA-02-0099-01A-01 2 0.4313 0.6353 0.008 0.716 0.260 0.000 0.016
#> TCGA-02-0106-01A-01 2 0.4226 0.7315 0.000 0.764 0.176 0.000 0.060
#> TCGA-02-0107-01A-01 2 0.0609 0.8720 0.000 0.980 0.000 0.000 0.020
#> TCGA-02-0111-01A-01 2 0.0566 0.8712 0.000 0.984 0.000 0.004 0.012
#> TCGA-02-0326-01A-01 5 0.4216 0.5874 0.032 0.080 0.052 0.012 0.824
#> TCGA-02-0337-01A-01 2 0.4102 0.5856 0.000 0.692 0.004 0.004 0.300
#> TCGA-06-0122-01A-01 3 0.4757 0.6898 0.000 0.148 0.732 0.000 0.120
#> TCGA-06-0124-01A-01 2 0.4740 0.0782 0.000 0.516 0.468 0.000 0.016
#> TCGA-06-0130-01A-01 2 0.0000 0.8734 0.000 1.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0324 0.8729 0.000 0.992 0.000 0.004 0.004
#> TCGA-06-0143-01A-01 2 0.5067 0.6269 0.000 0.700 0.172 0.000 0.128
#> TCGA-06-0147-01A-01 2 0.0609 0.8724 0.000 0.980 0.000 0.000 0.020
#> TCGA-06-0149-01A-05 2 0.2694 0.8352 0.000 0.888 0.032 0.004 0.076
#> TCGA-06-0152-01A-02 5 0.5175 0.2795 0.000 0.320 0.008 0.044 0.628
#> TCGA-06-0154-01A-02 2 0.1502 0.8597 0.000 0.940 0.056 0.000 0.004
#> TCGA-06-0164-01A-01 2 0.1041 0.8681 0.000 0.964 0.032 0.000 0.004
#> TCGA-06-0175-01A-01 2 0.4973 0.2964 0.000 0.564 0.408 0.004 0.024
#> TCGA-06-0176-01A-03 2 0.1872 0.8593 0.000 0.928 0.052 0.000 0.020
#> TCGA-06-0184-01A-01 2 0.2341 0.8488 0.000 0.912 0.012 0.056 0.020
#> TCGA-06-0189-01A-05 2 0.1780 0.8587 0.000 0.940 0.008 0.024 0.028
#> TCGA-06-0190-01A-01 2 0.0290 0.8735 0.000 0.992 0.008 0.000 0.000
#> TCGA-06-0194-01A-01 2 0.0162 0.8735 0.000 0.996 0.004 0.000 0.000
#> TCGA-06-0197-01A-02 2 0.0960 0.8709 0.000 0.972 0.004 0.008 0.016
#> TCGA-06-0210-01A-01 2 0.3762 0.6616 0.000 0.748 0.244 0.004 0.004
#> TCGA-06-0397-01A-01 2 0.3728 0.6782 0.000 0.748 0.244 0.000 0.008
#> TCGA-06-0409-01A-02 2 0.0865 0.8717 0.000 0.972 0.004 0.000 0.024
#> TCGA-06-0412-01A-01 2 0.4531 0.2794 0.000 0.568 0.424 0.004 0.004
#> TCGA-06-0644-01A-02 2 0.1310 0.8705 0.000 0.956 0.020 0.000 0.024
#> TCGA-06-0645-01A-01 2 0.0794 0.8713 0.000 0.972 0.000 0.000 0.028
#> TCGA-08-0346-01A-01 2 0.0794 0.8719 0.000 0.972 0.000 0.000 0.028
#> TCGA-08-0352-01A-01 3 0.4385 0.6921 0.000 0.180 0.752 0.000 0.068
#> TCGA-08-0360-01A-01 2 0.0510 0.8729 0.000 0.984 0.000 0.000 0.016
#> TCGA-08-0390-01A-01 2 0.1074 0.8697 0.000 0.968 0.004 0.016 0.012
#> TCGA-08-0392-01A-01 2 0.3829 0.7669 0.000 0.816 0.024 0.024 0.136
#> TCGA-08-0509-01A-01 2 0.1082 0.8706 0.000 0.964 0.008 0.000 0.028
#> TCGA-08-0510-01A-01 3 0.3883 0.6216 0.000 0.244 0.744 0.004 0.008
#> TCGA-08-0512-01A-01 2 0.0324 0.8736 0.000 0.992 0.004 0.000 0.004
#> TCGA-08-0522-01A-01 2 0.0579 0.8740 0.000 0.984 0.008 0.000 0.008
#> TCGA-12-0619-01A-01 2 0.0162 0.8735 0.000 0.996 0.000 0.000 0.004
#> TCGA-12-0620-01A-01 2 0.3550 0.6900 0.000 0.760 0.000 0.004 0.236
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA-02-0003-01A-01 1 0.1367 0.7390 0.944 0.000 0.000 0.012 0.044 0.000
#> TCGA-02-0010-01A-01 1 0.3244 0.7585 0.732 0.000 0.000 0.000 0.268 0.000
#> TCGA-02-0011-01B-01 1 0.3899 0.6395 0.592 0.000 0.000 0.000 0.404 0.004
#> TCGA-02-0014-01A-01 1 0.2664 0.7663 0.816 0.000 0.000 0.000 0.184 0.000
#> TCGA-02-0024-01B-01 1 0.3309 0.7548 0.720 0.000 0.000 0.000 0.280 0.000
#> TCGA-02-0026-01B-01 1 0.3371 0.7499 0.708 0.000 0.000 0.000 0.292 0.000
#> TCGA-02-0028-01A-01 1 0.1075 0.7407 0.952 0.000 0.000 0.000 0.048 0.000
#> TCGA-02-0046-01A-01 1 0.2300 0.7607 0.856 0.000 0.000 0.000 0.144 0.000
#> TCGA-02-0047-01A-01 5 0.7293 -0.0508 0.052 0.168 0.000 0.344 0.400 0.036
#> TCGA-02-0048-01A-01 1 0.1082 0.7341 0.956 0.000 0.004 0.000 0.040 0.000
#> TCGA-02-0060-01A-01 5 0.4530 0.3834 0.108 0.000 0.004 0.160 0.724 0.004
#> TCGA-02-0069-01A-01 1 0.3288 0.7567 0.724 0.000 0.000 0.000 0.276 0.000
#> TCGA-02-0074-01A-01 1 0.3126 0.7637 0.752 0.000 0.000 0.000 0.248 0.000
#> TCGA-02-0080-01A-01 5 0.3710 0.4577 0.076 0.000 0.060 0.000 0.820 0.044
#> TCGA-02-0084-01A-03 5 0.4526 0.3390 0.004 0.096 0.068 0.008 0.776 0.048
#> TCGA-02-0087-01A-01 5 0.2420 0.4461 0.020 0.000 0.060 0.012 0.900 0.008
#> TCGA-02-0104-01A-01 1 0.1148 0.6959 0.960 0.000 0.000 0.004 0.016 0.020
#> TCGA-02-0114-01A-01 1 0.0363 0.7134 0.988 0.000 0.000 0.000 0.012 0.000
#> TCGA-02-0281-01A-01 1 0.3390 0.7478 0.704 0.000 0.000 0.000 0.296 0.000
#> TCGA-02-0321-01A-01 6 0.3815 0.6295 0.024 0.040 0.000 0.008 0.120 0.808
#> TCGA-02-0325-01A-01 5 0.5053 0.4589 0.172 0.000 0.112 0.000 0.688 0.028
#> TCGA-02-0338-01A-01 1 0.2762 0.7667 0.804 0.000 0.000 0.000 0.196 0.000
#> TCGA-02-0339-01A-01 1 0.3446 0.7402 0.692 0.000 0.000 0.000 0.308 0.000
#> TCGA-02-0432-01A-02 5 0.3185 0.4528 0.128 0.000 0.012 0.016 0.836 0.008
#> TCGA-02-0439-01A-01 5 0.2730 0.4422 0.012 0.000 0.060 0.036 0.884 0.008
#> TCGA-02-0440-01A-01 1 0.3076 0.7643 0.760 0.000 0.000 0.000 0.240 0.000
#> TCGA-02-0446-01A-01 1 0.4285 0.4410 0.644 0.320 0.000 0.000 0.036 0.000
#> TCGA-06-0128-01A-01 4 0.5290 0.3846 0.128 0.000 0.000 0.596 0.272 0.004
#> TCGA-06-0129-01A-01 1 0.3499 0.7329 0.680 0.000 0.000 0.000 0.320 0.000
#> TCGA-06-0146-01A-01 1 0.3817 0.5987 0.568 0.000 0.000 0.000 0.432 0.000
#> TCGA-06-0156-01A-01 1 0.3151 0.7628 0.748 0.000 0.000 0.000 0.252 0.000
#> TCGA-06-0166-01A-01 1 0.0508 0.7214 0.984 0.012 0.000 0.000 0.004 0.000
#> TCGA-06-0174-01A-01 1 0.0146 0.7186 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-06-0177-01A-01 1 0.3428 0.7429 0.696 0.000 0.000 0.000 0.304 0.000
#> TCGA-06-0238-01A-02 4 0.5223 0.2556 0.000 0.000 0.000 0.540 0.104 0.356
#> TCGA-06-0241-01A-02 1 0.0777 0.7124 0.972 0.000 0.000 0.024 0.004 0.000
#> TCGA-06-0410-01A-01 1 0.5997 0.1520 0.564 0.000 0.008 0.284 0.032 0.112
#> TCGA-06-0413-01A-01 1 0.3371 0.7500 0.708 0.000 0.000 0.000 0.292 0.000
#> TCGA-06-0414-01A-01 1 0.0260 0.7163 0.992 0.000 0.000 0.000 0.008 0.000
#> TCGA-06-0646-01A-01 1 0.4322 0.3583 0.600 0.372 0.000 0.000 0.028 0.000
#> TCGA-06-0648-01A-01 1 0.5362 0.4905 0.524 0.000 0.000 0.000 0.356 0.120
#> TCGA-08-0245-01A-01 1 0.0146 0.7186 0.996 0.000 0.000 0.000 0.004 0.000
#> TCGA-08-0344-01A-01 1 0.3446 0.7417 0.692 0.000 0.000 0.000 0.308 0.000
#> TCGA-08-0347-01A-01 1 0.5933 0.4056 0.468 0.104 0.012 0.000 0.404 0.012
#> TCGA-08-0348-01A-01 1 0.3652 0.7278 0.672 0.000 0.000 0.000 0.324 0.004
#> TCGA-08-0350-01A-01 5 0.5418 -0.2176 0.388 0.000 0.000 0.000 0.492 0.120
#> TCGA-08-0353-01A-01 1 0.2362 0.6443 0.860 0.000 0.136 0.000 0.004 0.000
#> TCGA-08-0359-01A-01 5 0.4875 -0.3293 0.404 0.000 0.000 0.044 0.544 0.008
#> TCGA-08-0385-01A-01 1 0.5051 0.6178 0.596 0.000 0.000 0.000 0.300 0.104
#> TCGA-08-0517-01A-01 1 0.1196 0.7089 0.952 0.000 0.040 0.000 0.008 0.000
#> TCGA-08-0524-01A-01 1 0.1204 0.7397 0.944 0.000 0.000 0.000 0.056 0.000
#> TCGA-12-0616-01A-01 1 0.2968 0.6253 0.852 0.000 0.000 0.052 0.004 0.092
#> TCGA-12-0618-01A-01 1 0.3547 0.7460 0.696 0.000 0.000 0.000 0.300 0.004
#> TCGA-02-0089-01A-01 4 0.2030 0.7782 0.000 0.016 0.036 0.924 0.016 0.008
#> TCGA-02-0113-01A-01 4 0.5093 0.3765 0.000 0.000 0.372 0.560 0.052 0.016
#> TCGA-02-0115-01A-01 4 0.2333 0.7681 0.000 0.000 0.060 0.896 0.040 0.004
#> TCGA-02-0451-01A-01 4 0.3164 0.7292 0.000 0.084 0.012 0.856 0.036 0.012
#> TCGA-06-0132-01A-02 4 0.4468 0.6515 0.000 0.084 0.000 0.748 0.140 0.028
#> TCGA-06-0133-01A-02 4 0.0458 0.7817 0.000 0.000 0.000 0.984 0.016 0.000
#> TCGA-06-0138-01A-02 4 0.1257 0.7837 0.000 0.000 0.000 0.952 0.020 0.028
#> TCGA-06-0160-01A-01 4 0.4633 0.2176 0.024 0.000 0.000 0.500 0.468 0.008
#> TCGA-06-0162-01A-01 4 0.2213 0.7680 0.000 0.008 0.000 0.888 0.004 0.100
#> TCGA-06-0167-01A-01 4 0.4078 0.5651 0.008 0.000 0.000 0.676 0.300 0.016
#> TCGA-06-0171-01A-02 4 0.0972 0.7840 0.000 0.000 0.000 0.964 0.008 0.028
#> TCGA-06-0173-01A-01 4 0.6504 0.4883 0.168 0.000 0.156 0.592 0.048 0.036
#> TCGA-06-0179-01A-02 4 0.0790 0.7794 0.000 0.000 0.000 0.968 0.032 0.000
#> TCGA-06-0182-01A-01 4 0.3951 0.7154 0.000 0.000 0.036 0.796 0.056 0.112
#> TCGA-06-0185-01A-01 4 0.2901 0.7577 0.000 0.000 0.056 0.872 0.032 0.040
#> TCGA-06-0195-01B-01 4 0.0858 0.7797 0.000 0.000 0.000 0.968 0.028 0.004
#> TCGA-06-0208-01B-01 4 0.1890 0.7772 0.000 0.000 0.008 0.924 0.024 0.044
#> TCGA-06-0214-01A-02 4 0.1779 0.7838 0.000 0.020 0.004 0.936 0.020 0.020
#> TCGA-06-0219-01A-01 4 0.2358 0.7597 0.000 0.000 0.000 0.876 0.016 0.108
#> TCGA-06-0221-01A-01 4 0.1895 0.7805 0.000 0.000 0.000 0.912 0.016 0.072
#> TCGA-06-0237-01A-02 4 0.1196 0.7833 0.000 0.000 0.000 0.952 0.008 0.040
#> TCGA-06-0240-01A-02 4 0.1152 0.7761 0.000 0.000 0.000 0.952 0.044 0.004
#> TCGA-08-0349-01A-01 4 0.7163 0.1136 0.128 0.092 0.000 0.396 0.016 0.368
#> TCGA-08-0380-01A-01 4 0.5480 0.4654 0.000 0.224 0.000 0.628 0.120 0.028
#> TCGA-08-0386-01A-01 3 0.2428 0.7060 0.024 0.000 0.904 0.020 0.044 0.008
#> TCGA-08-0520-01A-01 4 0.3144 0.7260 0.000 0.000 0.004 0.808 0.016 0.172
#> TCGA-02-0007-01A-01 3 0.2309 0.7129 0.012 0.000 0.908 0.016 0.052 0.012
#> TCGA-02-0009-01A-01 3 0.2454 0.7387 0.000 0.000 0.840 0.000 0.160 0.000
#> TCGA-02-0016-01A-01 3 0.3078 0.7150 0.000 0.000 0.796 0.000 0.192 0.012
#> TCGA-02-0021-01A-01 3 0.0260 0.7514 0.000 0.000 0.992 0.000 0.008 0.000
#> TCGA-02-0023-01B-01 5 0.6054 -0.0828 0.000 0.000 0.260 0.000 0.392 0.348
#> TCGA-02-0027-01A-01 5 0.4997 0.4277 0.088 0.004 0.264 0.000 0.640 0.004
#> TCGA-02-0038-01A-01 3 0.2968 0.6648 0.000 0.000 0.852 0.092 0.052 0.004
#> TCGA-02-0043-01A-01 3 0.3278 0.7072 0.088 0.000 0.824 0.000 0.088 0.000
#> TCGA-02-0070-01A-01 3 0.2948 0.7212 0.000 0.000 0.804 0.000 0.188 0.008
#> TCGA-02-0102-01A-01 3 0.2048 0.7529 0.000 0.000 0.880 0.000 0.120 0.000
#> TCGA-02-0260-01A-03 5 0.6681 0.1678 0.048 0.000 0.280 0.000 0.448 0.224
#> TCGA-02-0269-01B-01 5 0.6017 0.0776 0.000 0.000 0.316 0.000 0.424 0.260
#> TCGA-02-0285-01A-01 3 0.3608 0.7126 0.000 0.000 0.788 0.000 0.148 0.064
#> TCGA-02-0289-01A-01 3 0.5758 0.1783 0.000 0.000 0.476 0.000 0.340 0.184
#> TCGA-02-0290-01A-01 6 0.2244 0.6125 0.000 0.048 0.012 0.016 0.012 0.912
#> TCGA-02-0317-01A-01 6 0.5887 0.0729 0.000 0.000 0.204 0.000 0.364 0.432
#> TCGA-02-0333-01A-02 5 0.6071 0.0487 0.000 0.000 0.336 0.000 0.392 0.272
#> TCGA-02-0422-01A-01 3 0.1334 0.7554 0.000 0.000 0.948 0.000 0.032 0.020
#> TCGA-02-0430-01A-01 3 0.1370 0.7352 0.004 0.000 0.948 0.012 0.036 0.000
#> TCGA-06-0125-01A-01 3 0.2631 0.7417 0.008 0.000 0.840 0.000 0.152 0.000
#> TCGA-06-0126-01A-01 3 0.4247 0.6006 0.040 0.000 0.688 0.000 0.268 0.004
#> TCGA-06-0137-01A-03 3 0.2738 0.7301 0.000 0.000 0.820 0.000 0.176 0.004
#> TCGA-06-0145-01A-04 3 0.2631 0.7305 0.000 0.000 0.820 0.000 0.180 0.000
#> TCGA-06-0148-01A-01 3 0.3284 0.7189 0.000 0.000 0.800 0.000 0.168 0.032
#> TCGA-06-0187-01A-01 3 0.1760 0.7195 0.000 0.000 0.928 0.020 0.048 0.004
#> TCGA-06-0211-01B-01 3 0.4789 0.4626 0.000 0.000 0.668 0.256 0.056 0.020
#> TCGA-06-0402-01A-01 3 0.2721 0.6968 0.028 0.000 0.888 0.024 0.052 0.008
#> TCGA-08-0246-01A-01 3 0.0993 0.7377 0.000 0.000 0.964 0.012 0.024 0.000
#> TCGA-08-0354-01A-01 6 0.3943 0.4710 0.000 0.084 0.000 0.156 0.000 0.760
#> TCGA-08-0355-01A-01 3 0.5870 0.0628 0.000 0.000 0.436 0.000 0.364 0.200
#> TCGA-08-0357-01A-01 3 0.2624 0.7479 0.000 0.000 0.856 0.000 0.124 0.020
#> TCGA-08-0358-01A-01 6 0.3198 0.6210 0.000 0.008 0.000 0.008 0.188 0.796
#> TCGA-08-0375-01A-01 3 0.6172 0.1597 0.304 0.000 0.528 0.000 0.112 0.056
#> TCGA-08-0511-01A-01 3 0.1814 0.7570 0.000 0.000 0.900 0.000 0.100 0.000
#> TCGA-08-0514-01A-01 3 0.0551 0.7506 0.000 0.000 0.984 0.004 0.008 0.004
#> TCGA-08-0518-01A-01 3 0.1814 0.7568 0.000 0.000 0.900 0.000 0.100 0.000
#> TCGA-08-0529-01A-02 3 0.1757 0.7587 0.000 0.000 0.916 0.000 0.076 0.008
#> TCGA-08-0531-01A-01 3 0.1340 0.7545 0.000 0.000 0.948 0.004 0.040 0.008
#> TCGA-02-0057-01A-01 5 0.6486 -0.0580 0.000 0.316 0.320 0.000 0.348 0.016
#> TCGA-02-0004-01A-01 2 0.1973 0.8490 0.000 0.916 0.012 0.004 0.004 0.064
#> TCGA-02-0006-01B-01 2 0.1453 0.8567 0.000 0.944 0.008 0.000 0.008 0.040
#> TCGA-02-0025-01A-01 2 0.1141 0.8596 0.000 0.948 0.000 0.000 0.000 0.052
#> TCGA-02-0033-01A-01 2 0.0260 0.8657 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-02-0034-01A-01 2 0.0547 0.8653 0.000 0.980 0.000 0.000 0.000 0.020
#> TCGA-02-0039-01A-01 2 0.0458 0.8649 0.000 0.984 0.000 0.000 0.000 0.016
#> TCGA-02-0051-01A-01 2 0.5460 0.5686 0.000 0.636 0.076 0.008 0.032 0.248
#> TCGA-02-0054-01A-01 2 0.4181 0.4794 0.000 0.600 0.384 0.000 0.012 0.004
#> TCGA-02-0055-01A-01 2 0.1285 0.8564 0.000 0.944 0.000 0.004 0.000 0.052
#> TCGA-02-0059-01A-01 2 0.2913 0.7745 0.000 0.812 0.000 0.004 0.004 0.180
#> TCGA-02-0064-01A-01 2 0.2400 0.8287 0.000 0.896 0.064 0.000 0.016 0.024
#> TCGA-02-0075-01A-01 3 0.4303 0.0423 0.000 0.460 0.524 0.000 0.012 0.004
#> TCGA-02-0079-01A-03 2 0.4650 0.5270 0.000 0.676 0.000 0.000 0.104 0.220
#> TCGA-02-0085-01A-01 2 0.1421 0.8554 0.000 0.944 0.000 0.000 0.028 0.028
#> TCGA-02-0086-01A-01 2 0.4947 0.6843 0.000 0.724 0.160 0.012 0.044 0.060
#> TCGA-02-0099-01A-01 2 0.2378 0.7825 0.000 0.848 0.152 0.000 0.000 0.000
#> TCGA-02-0106-01A-01 2 0.6143 0.5394 0.000 0.608 0.180 0.012 0.052 0.148
#> TCGA-02-0107-01A-01 2 0.0891 0.8618 0.000 0.968 0.000 0.000 0.008 0.024
#> TCGA-02-0111-01A-01 2 0.0692 0.8640 0.000 0.976 0.000 0.004 0.000 0.020
#> TCGA-02-0326-01A-01 6 0.4119 0.4991 0.000 0.004 0.008 0.004 0.348 0.636
#> TCGA-02-0337-01A-01 2 0.2608 0.8043 0.000 0.872 0.000 0.000 0.080 0.048
#> TCGA-06-0122-01A-01 3 0.3974 0.6951 0.000 0.032 0.744 0.000 0.212 0.012
#> TCGA-06-0124-01A-01 2 0.4432 0.1892 0.000 0.544 0.432 0.000 0.020 0.004
#> TCGA-06-0130-01A-01 2 0.0000 0.8656 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-06-0139-01A-01 2 0.0603 0.8639 0.000 0.980 0.000 0.000 0.004 0.016
#> TCGA-06-0143-01A-01 2 0.4323 0.6758 0.000 0.744 0.048 0.000 0.180 0.028
#> TCGA-06-0147-01A-01 2 0.0891 0.8618 0.000 0.968 0.000 0.000 0.008 0.024
#> TCGA-06-0149-01A-05 2 0.2349 0.8308 0.000 0.892 0.008 0.000 0.080 0.020
#> TCGA-06-0152-01A-02 6 0.4733 0.5807 0.000 0.044 0.000 0.024 0.264 0.668
#> TCGA-06-0154-01A-02 2 0.1644 0.8531 0.000 0.932 0.052 0.000 0.004 0.012
#> TCGA-06-0164-01A-01 2 0.0405 0.8669 0.000 0.988 0.008 0.000 0.000 0.004
#> TCGA-06-0175-01A-01 3 0.4596 0.3364 0.000 0.340 0.616 0.000 0.036 0.008
#> TCGA-06-0176-01A-03 2 0.2265 0.8413 0.000 0.896 0.024 0.004 0.000 0.076
#> TCGA-06-0184-01A-01 2 0.3424 0.6696 0.000 0.772 0.000 0.204 0.000 0.024
#> TCGA-06-0189-01A-05 2 0.1700 0.8465 0.000 0.916 0.000 0.004 0.000 0.080
#> TCGA-06-0190-01A-01 2 0.0260 0.8657 0.000 0.992 0.000 0.000 0.000 0.008
#> TCGA-06-0194-01A-01 2 0.0146 0.8657 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-06-0197-01A-02 2 0.1299 0.8603 0.000 0.952 0.004 0.004 0.004 0.036
#> TCGA-06-0210-01A-01 2 0.4273 0.5400 0.000 0.648 0.324 0.000 0.012 0.016
#> TCGA-06-0397-01A-01 2 0.4052 0.6404 0.000 0.708 0.260 0.000 0.020 0.012
#> TCGA-06-0409-01A-02 2 0.1049 0.8601 0.000 0.960 0.000 0.000 0.008 0.032
#> TCGA-06-0412-01A-01 3 0.4191 0.2444 0.000 0.388 0.596 0.000 0.012 0.004
#> TCGA-06-0644-01A-02 2 0.3965 0.7591 0.000 0.784 0.076 0.004 0.008 0.128
#> TCGA-06-0645-01A-01 2 0.1049 0.8602 0.000 0.960 0.000 0.000 0.008 0.032
#> TCGA-08-0346-01A-01 2 0.0363 0.8662 0.000 0.988 0.000 0.000 0.000 0.012
#> TCGA-08-0352-01A-01 3 0.4086 0.6813 0.000 0.124 0.752 0.000 0.124 0.000
#> TCGA-08-0360-01A-01 2 0.0972 0.8613 0.000 0.964 0.000 0.000 0.008 0.028
#> TCGA-08-0390-01A-01 2 0.1297 0.8614 0.000 0.948 0.000 0.012 0.000 0.040
#> TCGA-08-0392-01A-01 6 0.4622 0.2261 0.000 0.356 0.008 0.016 0.012 0.608
#> TCGA-08-0509-01A-01 2 0.1564 0.8517 0.000 0.936 0.000 0.000 0.024 0.040
#> TCGA-08-0510-01A-01 3 0.2723 0.6656 0.000 0.128 0.852 0.000 0.016 0.004
#> TCGA-08-0512-01A-01 2 0.0146 0.8657 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-08-0522-01A-01 2 0.0146 0.8659 0.000 0.996 0.000 0.000 0.000 0.004
#> TCGA-12-0619-01A-01 2 0.0000 0.8656 0.000 1.000 0.000 0.000 0.000 0.000
#> TCGA-12-0620-01A-01 2 0.4325 0.5686 0.000 0.692 0.000 0.000 0.064 0.244
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n subtype(p) k
#> ATC:NMF 170 6.82e-25 2
#> ATC:NMF 166 4.07e-46 3
#> ATC:NMF 106 1.24e-37 4
#> ATC:NMF 143 1.26e-67 5
#> ATC:NMF 132 7.69e-69 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
sessionInfo()
#> R version 3.6.0 (2019-04-26)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS: /usr/lib64/libblas.so.3.4.2
#> LAPACK: /usr/lib64/liblapack.so.3.4.2
#>
#> locale:
#> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8
#> [4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
#> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] genefilter_1.66.0 ComplexHeatmap_2.3.1 markdown_1.1 knitr_1.26
#> [5] GetoptLong_0.1.7 cola_1.3.2
#>
#> loaded via a namespace (and not attached):
#> [1] circlize_0.4.8 shape_1.4.4 xfun_0.11 slam_0.1-46
#> [5] lattice_0.20-38 splines_3.6.0 colorspace_1.4-1 vctrs_0.2.0
#> [9] stats4_3.6.0 blob_1.2.0 XML_3.98-1.20 survival_2.44-1.1
#> [13] rlang_0.4.2 pillar_1.4.2 DBI_1.0.0 BiocGenerics_0.30.0
#> [17] bit64_0.9-7 RColorBrewer_1.1-2 matrixStats_0.55.0 stringr_1.4.0
#> [21] GlobalOptions_0.1.1 evaluate_0.14 memoise_1.1.0 Biobase_2.44.0
#> [25] IRanges_2.18.3 parallel_3.6.0 AnnotationDbi_1.46.1 highr_0.8
#> [29] Rcpp_1.0.3 xtable_1.8-4 backports_1.1.5 S4Vectors_0.22.1
#> [33] annotate_1.62.0 skmeans_0.2-11 bit_1.1-14 microbenchmark_1.4-7
#> [37] brew_1.0-6 impute_1.58.0 rjson_0.2.20 png_0.1-7
#> [41] digest_0.6.23 stringi_1.4.3 polyclip_1.10-0 clue_0.3-57
#> [45] tools_3.6.0 bitops_1.0-6 magrittr_1.5 eulerr_6.0.0
#> [49] RCurl_1.95-4.12 RSQLite_2.1.4 tibble_2.1.3 cluster_2.1.0
#> [53] crayon_1.3.4 pkgconfig_2.0.3 zeallot_0.1.0 Matrix_1.2-17
#> [57] xml2_1.2.2 httr_1.4.1 R6_2.4.1 mclust_5.4.5
#> [61] compiler_3.6.0