getMsigdbIDF: Retrieve MSigDB data hosted on the hub

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

Retrieve MSigDB data hosted on the hub

Description

Download molecular signatures database (MSigDB) hosted on the ExperimentHub or retrieve pre-downloaded version from cache. This package currently hosts versions greater than 7.2 for human and mouse with both symbol and Entrez identifiers.

Usage

getMsigdbIDF(org = c("hs", "mm"), version = getMsigdbVersions())

Arguments

org	a character, representing the organism whose signature database needs to be retrieved ("hs" for human and "mm" for mouse).
version	a character, stating the version of MSigDB to be retrieved (should be >= 7.2). See getMsigdbVersions().

Value

a list of named numeric vectors, containing inverse document frequency (IDF) weights. Names represent terms that the IDF is computed for. IDFs are computed using gene-set names ("Name") and short descriptions ("Short").

Examples

gsc = getMsigdbIDF("hs")

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