msigdbr {msigdbr}

Retrieve the gene sets data frame

Description

Retrieve a data frame of gene sets and their member genes. The available species and collections can be checked with msigdbr_species() and msigdbr_collections().

Usage

msigdbr(species = "Homo sapiens", category = NULL, subcategory = NULL)

Arguments

species

Species name, such as Homo sapiens or Mus musculus.

category

MSigDB collection abbreviation, such as H or C1.

subcategory

MSigDB sub-collection abbreviation, such as CGP or BP.

Value

A data frame of gene sets with one gene per row.

References

https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp

Examples

# get all human gene sets

msigdbr(species = "Homo sapiens")


# get mouse C2 (curated) CGP (chemical and genetic perturbations) gene sets

msigdbr(species = "Mus musculus", category = "C2", subcategory = "CGP")