GeneNMF (version 0.8.0)

runGSEA: Run Gene set enrichment analysis

Description

Utility function to run Gene Set Enrichment Analysis (GSEA) against gene sets from MSigDB. Note: this is an optional function, which is conditional to the installation of suggested packages fgsea and msigdbr.

Usage

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

Value

Returns a table of enriched gene programs from GSEA

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()

custom.db

A custom database of signatures, to be used instead of MSigDB. Provide custom.db as a named list, where the list names are the signature names, and the list elements are the signatures (as vectors).

pval.thr

Min p-value to include results

Examples

data(sampleObj)
geneset <- c("BANK1","CD22","CD79A","CD19","IGHD","IGHG3","IGHM")
#test is conditional on availability of suggested packages
if (requireNamespace("fgsea", quietly=TRUE) &
   requireNamespace("msigdbr", quietly=TRUE)) {
   gsea_res <- runGSEA(geneset,
       universe=rownames(sampleObj),
       category = "C8")
}