runGSEA {RCAS}R Documentation

runGSEA

Description

This function is used to facilitate gene set enrichment analysis (GSEA) for a given set of genes

Usage

runGSEA(geneSetList, species = "human", backgroundGenes, targetedGenes)

Arguments

geneSetList

A named list of vectors where each vector consists of a set of Entrez gene ids (for instance, returned by parseMsigdb function)

species

A character string denoting the species under analysis. Options are 'human', 'mouse', 'fly' and 'worm'.

backgroundGenes

A vector of Ensembl gene ids that serve as background set of genes for GO term enrichment. In the context of RCAS, this should be the whole set of genes found in an input GTF file.

targetedGenes

A vector of Ensembl gene ids that serve as the set for which GSEA should be carried out. In the context of RCAS, this should be the set of genes that overlap the query regions

Value

A data.frame object containing enriched gene sets and associated statistics

Examples


#load test data
data(geneSets)
data(gff)
data(queryRegions)
#get all genes from the gff data
backgroundGenes <- unique(gff$gene_id)
#get genes that overlap query regions
overlaps <- queryGff(queryRegions, gff)
targetedGenes <- unique(overlaps$gene_id)
resultsGSEA <- runGSEA(geneSetList = geneSets,
          species = 'human',
          backgroundGenes = backgroundGenes,
          targetedGenes = targetedGenes)

[Package RCAS version 1.12.0 Index]