Load MSigDB genesets

Usage

get_MSigDB(
  cat = unique(msigdbr_collections()$gs_cat),
  to = "ENSEMBL",
  org = "hsa"
)

Arguments

cat: array of categories to load. Defaults to array of all MSigDB categories
to: convert gene names to this type using EnrichmentBrowser::idMap(). See EnrichmentBrowser::idTypes(org="hsa") for valid types
org: organism. human ('hsa'), mouse ('mmu'), etc

Value

Gene sets stored as GeneSetCollection

Details

This function loads the MSigDB gene sets using the packages EnrichmentBrowser and msigdbr. It can take a mintute to load because converting gene name type is slow.

Examples

# load Hallmark gene sets
gs = get_MSigDB('H')

# load all gene sets
# gs = get_MSigDB()