getMsigdb: Retrieve MSigDB data hosted on the hub

In DavisLaboratory/msigdbR: 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

getMsigdb(
  org = c("hs", "mm"),
  id = c("SYM", "EZID"),
  version = getMsigdbVersions()
)

Arguments

org	a character, representing the organism whose signature database needs to be retrieved ("hs" for human and "mm" for mouse).
id	a character, representing the ID type to use ("SYM" for gene symbols and "EZID" for Entrez IDs).
version	a character, stating the version of MSigDB to be retrieved (should be >= 7.2). See getMsigdbVersions().

Value

a GeneSetCollection, containing GeneSet objects from the specified version of the molecular signatures database (MSigDB).

Examples

gsc = getMsigdb('hs', 'SYM')

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