subsetCollection: Subset collections and sub-collections of MSigDB

In DavisLaboratory/msigdbR: An ExperimentHub Package for the Molecular Signatures Database (MSigDB)

Subset collections and sub-collections of MSigDB

Description

The molecular signatures database (MSigDB) is composed of collections and sub-collection. Many analyses (e.g. gene-set enrichment using limma::fry) are best carried out within specific collections rather than across the entire database of signatures. This function allows subsetting of MSigDB data objects within this package using collection and sub-collection types.

Usage

subsetCollection(gsc, collection = c(), subcollection = c())

Arguments

gsc	a GeneSetCollection object, containing MSigDB genesets in the form of GeneSet objects.
collection	a character, stating the collection(s) to be retrieved. The collection(s) must be one from the listCollections() function.
subcollection	a character, stating the sub-collection(s) to be retrieved. The sub-collection(s) must be one from the listSubCollections() function.

Value

a GeneSetCollection object, containing gene sets belonging to the queries collection and/or sub-collection.

Examples

gsc = getMsigdb('hs', 'SYM')
subsetCollection(gsc, collection = "h")

DavisLaboratory/msigdbR documentation built on July 27, 2023, 4 p.m.