refineSubpopulationLabels {PAC}

Refines the subpopulation labels from PAC using network alignment and small subpopulation information. Outputs a new set of files containing the representative labels.

Description

Refines the subpopulation labels from PAC using network alignment and small subpopulation information. Outputs a new set of files containing the representative labels.

Usage

refineSubpopulationLabels(sampleIDs, dim_subset, clades_network_only,
  expressionGroupClamp)

Arguments

sampleIDs

sampleID vector

dim_subset

a string vector of string names to subset the data columns for PAC; set to NULL to use all columns

clades_network_only

the alignment results from MAN; used to translate the original sample-specific labels into clade labels

expressionGroupClamp

clamps the subpopulations into desired number of expression groups for assigning small subpopulations into larger groups or their own groups.