gatherGeneSets: Gather Named Sets of Genes

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Gather Named Sets of Genes

Description

A flexible way to gather named collections of gene sets for pathway enrichment and differential expression.

Usage

gatherGeneSets(geneSets, descriptor = "GeneSets", mode = c("combined", "separate"))

Arguments

geneSets	a character vector of object names of pre-defined gene sets, as from pathway definitions; or a list of vectors of gene names
descriptor	if geneSets is a list, the prefix to attach to each list element.
mode	if geneSets is a character vector, controls whether all geneSets are merged into one large combined set.

Details

This is a low level function shared by link{geneSetEnrichment} and other pathways tools. It turns named pathway definition objects into the list(s) of genes needed for pathway analysis.

When given a character vector of pathway object names, this relies on the current species getCurrentSpecies to load the appropriate files.

Value

a LIST with objects

n	Number of lists of geneSets returned
descriptor	descriptor name for each list
geneSets	a list of geneSets, each ready for use by a pathway enrichment algorithm

See Also

See Also geneSetEnrichment, link{pipe.GeneSetAnalysis}

robertdouglasmorrison/DuffyTools documentation built on April 16, 2024, 6:31 a.m.