getMsigIdType: Infer gene identifier type for the gene set collection

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

Infer gene identifier type for the gene set collection

Description

The gene identifier (Symbol or Entrez ID) of a gene set collection is inferred from the IDs present in the data. A collection should ideally store gene sets using a single identifier type. This function returns the identifier type (either SymbolIdentifier or EntrezIdentifier) of the collection. It returns an error if the identifier is neither of these.

Usage

getMsigIdType(gsc)

Arguments

gsc	a GeneSetCollection object, containing MSigDB genesets in the form of GeneSet objects.

Value

a GSEABase::SymbolIdentifier or GSEABASE::EntrezIdentifier object, specifying the gene identifier type (gene symbols or Entrez IDs respectively).

Examples

gsc <- getMsigdb()
id <- getMsigIdType(gsc)

DavisLaboratory/msigdb documentation built on July 18, 2023, 7:54 p.m.