test_to_known_factors-ConsensusPartition-method.RdTest correspondance between predicted subgroups and known factors
# S4 method for ConsensusPartition
test_to_known_factors(object, k, known = get_anno(object),
silhouette_cutoff = 0.5, verbose = FALSE)A ConsensusPartition-class object.
Number of subgroups. It uses all k if it is not specified.
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 it are omit.
Whether to print messages.
The test is performed by test_between_factors between the predicted classes and user's annotation table.
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.
data(golub_cola)
res = golub_cola["ATC:skmeans"]
anno = get_anno(res)
anno
#> ALL.AML
#> 39 ALL
#> 40 ALL
#> 42 ALL
#> 47 ALL
#> 48 ALL
#> 49 ALL
#> 41 ALL
#> 43 ALL
#> 44 ALL
#> 45 ALL
#> 46 ALL
#> 70 ALL
#> 71 ALL
#> 72 ALL
#> 68 ALL
#> 69 ALL
#> 67 ALL
#> 55 ALL
#> 56 ALL
#> 59 ALL
#> 52 AML
#> 53 AML
#> 51 AML
#> 50 AML
#> 54 AML
#> 57 AML
#> 58 AML
#> 60 AML
#> 61 AML
#> 65 AML
#> 66 AML
#> 63 AML
#> 64 AML
#> 62 AML
#> 1 ALL
#> 2 ALL
#> 3 ALL
#> 4 ALL
#> 5 ALL
#> 6 ALL
#> 7 ALL
#> 8 ALL
#> 9 ALL
#> 10 ALL
#> 11 ALL
#> 12 ALL
#> 13 ALL
#> 14 ALL
#> 15 ALL
#> 16 ALL
#> 17 ALL
#> 18 ALL
#> 19 ALL
#> 20 ALL
#> 21 ALL
#> 22 ALL
#> 23 ALL
#> 24 ALL
#> 25 ALL
#> 26 ALL
#> 27 ALL
#> 34 AML
#> 35 AML
#> 36 AML
#> 37 AML
#> 38 AML
#> 28 AML
#> 29 AML
#> 30 AML
#> 31 AML
#> 32 AML
#> 33 AML
test_to_known_factors(res, k = 3)
#> n_sample ALL.AML(p-value) k
#> ATC:skmeans 72 1.826171e-10 3
# or explicitly specify known argument
test_to_known_factors(res, k = 3, known = anno)
#> n_sample ALL.AML(p-value) k
#> ATC:skmeans 72 1.826171e-10 3