get_mgsigdb_gsets: Retrieve Organism-specific MSigDB Gene Sets

In pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Retrieve Organism-specific MSigDB Gene Sets

Description

Retrieve Organism-specific MSigDB Gene Sets

Usage

get_mgsigdb_gsets(
  species = "Homo sapiens",
  db_species = "HS",
  collection = NULL,
  subcollection = NULL
)

Arguments

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.

Details

this function utilizes the function msigdbr from the msigdbr package to retrieve the 'Molecular Signatures Database' (MSigDB) gene sets (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>). Available collections are: H: hallmark gene sets, C1: positional gene sets, C2: curated gene sets, C3: motif gene sets, C4: computational gene sets, C5: GO gene sets, C6: oncogenic signatures and C7: immunologic signatures

Value

Retrieves the MSigDB gene sets and returns a list containing 2 elements:

• gene_sets - A list containing the genes involved in each of the selected MSigDB gene sets

• descriptions - A named vector containing the descriptions for each selected MSigDB gene set

pathfindR documentation built on Nov. 5, 2025, 5:59 p.m.