get_gene_sets_list {pathfindR}

Retrieve Organism-specific Gene Sets List

Description

Retrieve Organism-specific Gene Sets List

Usage

get_gene_sets_list(
  source = "KEGG",
  org_code = "hsa",
  species = "Homo sapiens",
  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

(Used for 'MSigDB' only) species name, such as Homo sapiens, Mus musculus, etc. See msigdbr_show_species for all the species available in the msigdbr package (default = 'Homo sapiens')

collection

(Used for 'MSigDB' only) collection. i.e., H, C1, C2, C3, C4, C5, C6, C7.

subcollection

(Used for 'MSigDB' only) sub-collection, such as CGP, MIR, BP, etc. (default = NULL, i.e. list all gene sets in collection)

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_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.