msigdbr (version 7.1.1)

msigdbr: Retrieve the msigdbr data frame

Description

Retrieve the msigdbr data frame

Usage

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

Arguments

species

Species name, such as Homo sapiens or Mus musculus. The available species can be retrieved with msigdbr_show_species().

category

MSigDB collection abbreviation, such as H, C1, C2, C3, C4, C5, C6, C7.

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

# NOT RUN {
# get all human gene sets
# }
# NOT RUN {
msigdbr(species = "Homo sapiens")
# }
# NOT RUN {
# get mouse C2 (curated) CGP (chemical and genetic perturbations) gene sets
# }
# NOT RUN {
msigdbr(species = "Mus musculus", category = "C2", subcategory = "CGP")
# }
# NOT RUN {
# check all the available categories and sub-categories
# }
# NOT RUN {
msigdbr() %>% dplyr::distinct(gs_cat, gs_subcat) %>% dplyr::arrange(gs_cat, gs_subcat)
# }