Retrieve Organism-specific Gene Sets List
get_gene_sets_list( source = "KEGG", org_code = "hsa", species = "Homo sapiens", collection, subcollection = NULL )
As of this version, either "KEGG", "Reactome" or "MSigDB" (default = "KEGG")
(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
(Used for "MSigDB" only) species name, such as Homo sapiens, Mus musculus, etc.
(Used for "MSigDB" only) collection. i.e., H, C1, C2, C3, C4, C5, C6, C7.
(Used for "MSigDB" only) sub-collection, such as CGP, MIR, BP, etc. (default = NULL, i.e. list all gene sets in collection)
A list containing 2 elements:
gene_setsA list containing the genes involved in each gene set
descriptionsA 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.
msigdbr_show_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.