parseMsigdb {RCAS}R Documentation

parseMsigdb

Description

A function to import gene sets downloaded from the Molecular Signatures Database (MSIGDB)

Usage

parseMsigdb(filePath)

Arguments

filePath

Path to a file containing gene sets from MSIGDB. The gene ids must be in Entrez format.

Value

A list of vectors where each vector consists of a set of Entrez gene ids

Examples

#First Download gene sets (with Entrez Ids) from MSIGDB database
#from \url{http://software.broadinstitute.org/gsea/msigdb/collections.jsp#C2}

input <- system.file('extdata', 'msigdb_test.gmt', package='RCAS')
msigDB <- parseMsigdb (filePath = input)


[Package RCAS version 1.12.0 Index]