test_to_known_factors-DownSamplingConsensusPartition-method {cola}R Documentation

Test correspondance between predicted subgroups and known factors

Description

Test correspondance between predicted subgroups and known factors

Usage

## S4 method for signature 'DownSamplingConsensusPartition'
test_to_known_factors(object, k, known = get_anno(object),
    p_cutoff = 0.05, verbose = FALSE)

Arguments

object

A DownSamplingConsensusPartition-class object.

k

Number of subgroups. It uses all k if it is not specified.

known

A vector or a data frame with known factors. By default it is the annotation table set in consensus_partition_by_down_sampling.

p_cutoff

Cutoff for p-values for the class prediction. Samples with p-value higher than it are omit.

verbose

Whether to print messages.

Details

The test is performed by test_between_factors between the predicted classes and user's annotation table.

Value

A data frame with the following columns:

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

data(golub_cola_ds)
test_to_known_factors(golub_cola_ds, k = 3)
test_to_known_factors(golub_cola_ds)

[Package cola version 2.0.0 Index]