refineSubpopulationLabels

sampleIDs

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

dim_subset

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

clades_network_only

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

expressionGroupClamp

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

Implements partition-assisted clustering and multiple alignments of networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set. Please see Li et al. (2017) <doi:10.1371/journal.pcbi.1005875> for detail method description.

Ye Li

Partition-Assisted Clustering and Multiple Alignments of
Networks

refineSubpopulationLabels function

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

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

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

Description

Usage

Arguments