get_mgsigdb_gsets {pathfindR}

Retrieve Organism-specific MSigDB Gene Sets

Description

Retrieve Organism-specific MSigDB Gene Sets

Usage

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

Arguments

species

species name, such as Homo sapiens, Mus musculus, etc. See msigdbr_show_species for all the species available in the msigdbr package

collection

collection. i.e., H, C1, C2, C3, C4, C5, C6, C7.

subcollection

sub-collection, such as CGP, BP, etc. (default = NULL, i.e. list all gene sets in collection)

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