test_to_known_factors-ConsensusPartition-method {cola} | R Documentation |
Test correspondance between predicted subgroups and known factors
## S4 method for signature 'ConsensusPartition' test_to_known_factors(object, k, known = get_anno(object), silhouette_cutoff = 0.5, verbose = FALSE)
object |
A |
k |
Number of subgroups. It uses all |
known |
A vector or a data frame with known factors. By default it is the annotation table set in |
silhouette_cutoff |
Cutoff for sihouette scores. Samples with value less than it are omit. |
verbose |
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.
Zuguang Gu <z.gu@dkfz.de>
data(golub_cola) res = golub_cola["ATC:skmeans"] anno = get_anno(res) anno test_to_known_factors(res, k = 3) # or explicitly specify known argument test_to_known_factors(res, k = 3, known = anno)