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

In ncborcherding/scone: Single-Cell Operation for Neat Enrichment

Description

This function allows users to select libraries and specific gene.sets from a list of GeneSetCollection objects.

This function allows users to select libraries and specific gene.sets from a list of GeneSetCollection objects accessed by .

Usage

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

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 libraries or multiple libraries to select, example: library = c("H", "C5").
gene.sets	Select gene sets or pathways, using specific names, example: pathways = c("HALLMARK_TNFA_SIGNALING_VIA_NFKB").
collection	A list of GeneSetCollection objects.

Value

List of GeneSets in collection format

List of GeneSets in collection format

Author(s)

Nick Borcherding, Jared Andrews

Nick Borcherding, Jared Andrews

Examples

gsea_library <- data(gsea_library)
GS <- getGeneSets(collection = gsea_library, library = "Hallmark")

GS <- getGeneSets(library = "H")

ncborcherding/scone documentation built on Sept. 5, 2020, 1:11 a.m.