test_to_known_factors-ConsensusPartitionList-method.RdTest correspondance between predicted classes and known factors
# S4 method for ConsensusPartitionList
test_to_known_factors(object, k, known = get_anno(object),
silhouette_cutoff = 0.5, verbose = FALSE)A ConsensusPartitionList-class object.
Number of subgroups. It uses all k if it is not set.
A vector or a data frame with known factors. By default it is the annotation table set in consensus_partition or run_all_consensus_partition_methods.
Cutoff for sihouette scores. Samples with value less than this are omit.
Whether to print messages.
The function basically sends each ConsensusPartition-class object to
test_to_known_factors,ConsensusPartition-method and merges results afterwards.
A data frame with the following columns:
number of samples used to test after filtered by silhouette_cutoff,
p-values from the tests,
number of subgroups.
If there are NA values, basically it means there are no efficient data points to perform the test.
data(golub_cola)
test_to_known_factors(golub_cola)
#> n_sample ALL.AML(p-value) k
#> SD:skmeans 72 3.256935e-13 2
#> SD:skmeans 69 6.082538e-14 3
#> SD:skmeans 57 6.112061e-10 4
#> SD:skmeans 60 6.592515e-10 5
#> SD:skmeans 60 4.259907e-10 6
#> CV:skmeans 71 9.787012e-14 2
#> CV:skmeans 66 1.481309e-12 3
#> CV:skmeans 58 6.372531e-11 4
#> CV:skmeans 49 3.517737e-09 5
#> CV:skmeans 51 5.083683e-09 6
#> MAD:skmeans 71 9.787012e-14 2
#> MAD:skmeans 69 3.422182e-13 3
#> MAD:skmeans 65 1.432104e-11 4
#> MAD:skmeans 51 1.066152e-08 5
#> MAD:skmeans 61 4.989276e-09 6
#> ATC:skmeans 72 1.505160e-04 2
#> ATC:skmeans 72 1.826171e-10 3
#> ATC:skmeans 70 2.170533e-09 4
#> ATC:skmeans 59 1.351324e-08 5
#> ATC:skmeans 46 7.476557e-07 6
#> SD:mclust 70 1.547171e-13 2
#> SD:mclust 72 8.542092e-14 3
#> SD:mclust 61 8.286055e-11 4
#> SD:mclust 65 5.349855e-11 5
#> SD:mclust 54 5.262681e-11 6
#> CV:mclust 71 1.101449e-13 2
#> CV:mclust 66 1.481309e-12 3
#> CV:mclust 55 1.139992e-12 4
#> CV:mclust 58 3.660309e-11 5
#> CV:mclust 65 4.130359e-11 6
#> MAD:mclust 70 1.733409e-13 2
#> MAD:mclust 68 5.882548e-13 3
#> MAD:mclust 66 8.880807e-12 4
#> MAD:mclust 65 6.031869e-11 5
#> MAD:mclust 60 5.508749e-10 6
#> ATC:mclust 72 1.574505e-02 2
#> ATC:mclust 67 6.537953e-04 3
#> ATC:mclust 58 7.968710e-06 4
#> ATC:mclust 65 6.286670e-10 5
#> ATC:mclust 60 4.838478e-09 6
#> SD:kmeans 72 6.197475e-14 2
#> SD:kmeans 70 3.557696e-14 3
#> SD:kmeans 50 5.607336e-10 4
#> SD:kmeans 35 2.028995e-06 5
#> SD:kmeans 45 3.975960e-09 6
#> CV:kmeans 72 5.108677e-13 2
#> CV:kmeans 68 6.926395e-13 3
#> CV:kmeans 34 4.139938e-08 4
#> CV:kmeans 55 1.882447e-10 5
#> CV:kmeans 59 1.256845e-10 6
#> MAD:kmeans 72 5.108677e-13 2
#> MAD:kmeans 64 3.743085e-12 3
#> MAD:kmeans 44 9.575551e-09 4
#> MAD:kmeans 59 6.096370e-10 5
#> MAD:kmeans 56 8.594749e-09 6
#> ATC:kmeans 70 2.718960e-04 2
#> ATC:kmeans 57 1.973871e-05 3
#> ATC:kmeans 60 1.155630e-06 4
#> ATC:kmeans 70 6.522482e-08 5
#> ATC:kmeans 66 2.039385e-07 6
#> SD:pam 72 5.108677e-13 2
#> SD:pam 63 7.411494e-12 3
#> SD:pam 62 1.060516e-11 4
#> SD:pam 59 1.929880e-10 5
#> SD:pam 52 4.256044e-09 6
#> CV:pam 69 1.757005e-10 2
#> CV:pam 58 1.840146e-12 3
#> CV:pam 67 9.171718e-13 4
#> CV:pam 57 1.034494e-10 5
#> CV:pam 26 1.608709e-04 6
#> MAD:pam 69 3.414214e-13 2
#> MAD:pam 60 4.847143e-12 3
#> MAD:pam 66 1.140267e-11 4
#> MAD:pam 66 3.563719e-11 5
#> MAD:pam 61 2.460744e-10 6
#> ATC:pam 70 8.115728e-07 2
#> ATC:pam 69 1.509330e-06 3
#> ATC:pam 71 1.518569e-05 4
#> ATC:pam 64 3.510948e-06 5
#> ATC:pam 48 7.882661e-06 6
#> SD:hclust 70 5.435049e-16 2
#> SD:hclust 68 1.713908e-15 3
#> SD:hclust 62 2.197099e-13 4
#> SD:hclust 53 8.521753e-11 5
#> SD:hclust 45 3.975960e-09 6
#> CV:hclust 67 2.755841e-15 2
#> CV:hclust 55 1.139992e-12 3
#> CV:hclust 43 4.599055e-10 4
#> CV:hclust 40 1.065509e-08 5
#> CV:hclust 36 2.893696e-07 6
#> MAD:hclust 69 6.975197e-15 2
#> MAD:hclust 59 1.542811e-13 3
#> MAD:hclust 29 5.043477e-07 4
#> MAD:hclust 33 3.220673e-07 5
#> MAD:hclust 51 8.648732e-10 6
#> ATC:hclust 66 7.528671e-05 2
#> ATC:hclust 57 8.433404e-05 3
#> ATC:hclust 57 7.720606e-03 4
#> ATC:hclust 54 1.021776e-05 5
#> ATC:hclust 54 1.021776e-05 6