Retrieve Organism-specific Gene Sets List

get_gene_sets_list(
  source = "KEGG",
  org_code = "hsa",
  species = "Homo sapiens",
  db_species = "HS",
  collection,
  subcollection = NULL
)

Arguments

source: As of this version, either 'KEGG', 'Reactome' or 'MSigDB' (default = 'KEGG')
org_code: (Used for 'KEGG' only) KEGG organism code for the selected organism. For a full list of all available organisms, see https://www.genome.jp/kegg/catalog/org_list.html
species: species name for output genes, such as Homo sapiens, Mus musculus, etc. See msigdbr_species for all the species available in the msigdbr package.
db_species: Species abbreviation for the human or mouse databases ("HS" or "MM").
collection: collection. e.g., H, C1. (default = NULL, i.e. list all gene sets in collection). See msigdbr_collections for all available options the msigdbr package.
subcollection: sub-collection, such as CGP, BP, etc. (default = NULL, i.e. list all gene sets in collection). See msigdbr_collections for all available options the msigdbr package.

Value

A list containing 2 elements:

gene_sets - A list containing the genes involved in each gene set
descriptions - A named vector containing the descriptions for each gene set

. For 'KEGG' and 'MSigDB', it is possible to choose a specific organism. For a full list of all available KEGG organisms, see https://www.genome.jp/kegg/catalog/org_list.html. See msigdbr_species for all the species available in the msigdbr package used for obtaining 'MSigDB' gene sets. For Reactome, there is only one collection of pathway gene sets.