get_gene_sets_list: Retrieve Organism-specific Gene Sets List

In pathfindR: Enrichment Analysis Utilizing Active Subnetworks

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_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_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.

pathfindR documentation built on April 3, 2025, 9:25 p.m.