get_MSigDB: Load MSigDB genesets

In GabrielHoffman/zenith: Gene set analysis following differential expression using linear (mixed) modeling with dream

Load MSigDB genesets

Description

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

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.

Value

Gene sets stored as GeneSetCollection

Examples

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

# load all gene sets
# gs = get_MSigDB()

GabrielHoffman/zenith documentation built on March 10, 2024, 11:43 p.m.