getGeneSets {escape}R Documentation

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, gene.sets = NULL)

Arguments

species

The scientific name of the species of interest in order to get correcent gene nomenclature

library

Individual collection(s) of gene sets, e.g. c("H", "C5"). See https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp for all MSigDB collections.

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 GeneSetCollection object containing the requested GeneSet objects.

Author(s)

Nick Borcherding, Jared Andrews

Examples

GS <- getGeneSets(library = "H")


[Package escape version 1.3.1 Index]