getMsigOrganism: Infer organism type for the gene set collection

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

Infer organism type for the gene set collection

Description

Since both Human and Mouse MSigDB collections are hosted in this package, this function infers the type of organism represented in a gene set collection based on the gene IDs present. If not all gene IDs belong to the same organism, the organism with more than 50% gene IDs present in the collection is returned. In any other case, the function returns an error.

Usage

getMsigOrganism(gsc, idType)

Arguments

gsc	a GeneSetCollection object, containing MSigDB genesets in the form of GeneSet objects.
idType	a GSEABase::SymbolIdentifier or GSEABASE::EntrezIdentifier object, representing the ID type inferred from the getMsigIdType() function. Avoid providing this manually.

Value

a character, either "mm" (representing Mus musculus - mouse) or "hs" (representing Homo sapiens - human).

Examples

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

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