runGSEA {GeneNMF}

Run Gene set enrichment analysis

Description

Utility function to run Gene set enrichment analysis (GSEA) against gene sets from MSigDB.

Usage

runGSEA(
  genes,
  universe = NULL,
  category = "H",
  subcategory = NULL,
  species = "Homo sapiens",
  pval.thr = 0.05
)

Arguments

genes

A vector of genes

universe

Background universe of gene symbols (passed on to fgsea::fora)

category

GSEA main category (e.g. "H" or "C5")

subcategory

GSEA subcategory

species

Species for GSEA analysis. For a list of the available species, type msigdbr::msigdbr_species()

pval.thr

Min p-value to include results

Value

Returns a table of enriched gene programs from GSEA

Examples

data(sampleObj)
geneset <- c("BANK1","CD22","CD79A","CD19","IGHD","IGHG3","IGHM")
gsea_res <- runGSEA(geneset, universe=rownames(sampleObj), category = "C8")