getGeneSets: Get a collection of gene sets to perform enrichment on

In ncborcherding/escape: Easy single cell analysis platform for enrichment

Get a collection of gene sets to perform enrichment on

Description

This function allows users to select libraries and specific gene.sets to form a GeneSetCollection that is a list of gene sets.

Usage

getGeneSets(
  species = "Homo sapiens",
  library = NULL,
  subcategory = NULL,
  gene.sets = NULL
)

Arguments

species	The scientific name of the species of interest in order to get correct gene nomenclature
library	Individual collection(s) of gene sets, e.g. c("H", "C5"). See msigdbrfor all MSigDB collections.
subcategory	MSigDB sub-collection abbreviation, such as CGP or BP.
gene.sets	Select gene sets or pathways, using specific names, example: pathways = c("HALLMARK_TNFA_SIGNALING_VIA_NFKB"). Will only be honored if library is set, too.

Value

A list of gene sets from msigdbr.

Author(s)

Nick Borcherding, Jared Andrews

Examples

GS <- getGeneSets(library = "H")

ncborcherding/escape documentation built on Sept. 23, 2024, 10:01 p.m.