get_geneSets_from_msigdbr: Get the gene-sets from the msigdbr package.

In massiveGST: Competitive Gene Sets Test with the Mann-Whitney-Wilcoxon Test

Get the gene-sets from the msigdbr package.

Description

This is a wrapper for extraction a gene-sets collection as a vector list to match the data structure for massiveGST function.

Usage

get_geneSets_from_msigdbr(category, what, subcategory = NULL, species = "Homo sapiens")

Arguments

category	MSigDB collection abbreviation, such as H or C1.
what	a character string specifying the code representation of the genes; must be one of "gene_symbol", "entrez_gene", "ensembl_gene", "human_gene_symbol", "human_entrez_gene", "human_ensembl_gene";
subcategory	MSigDB sub-collection abbreviation, such as CGP or BP; NULL (default)
species	Species name, such as 'Homo sapiens' or 'Mus musculus'.

Value

A vector list of gene-sets

Author(s)

Stefano M. Pagnotta

See Also

msigdbr

Examples

library(massiveGST)

# get the gene-sets
geneSets <- get_geneSets_from_msigdbr(category = "H", what = "gene_symbol")

class(geneSets)
head(geneSets, 3)

massiveGST documentation built on March 31, 2023, 8:59 p.m.