tempoR (version 1.0.4.4)

loadGMT: Load a Gene Matrix Transposed formatted file

Description

loadGMT loads a Gene Matrix Transposed formatted file from a text file to the data structure used by TEMPO. In the .gmt format, each row represents a gene set, with tab delimited columns. The first column is a gene set name, the second columns and optional description, and the remaining columns contain gene ids for each gene in the gene set. The format is also described at the BROAD site.

Usage

loadGMT(target)

Arguments

target

a string indicating the location of the .gmt file

Value

a list indexed by gene set name of lists of gene ids

Examples

# NOT RUN {
# An example collection of gene sets is included in the package in .gmt format
exampleGeneSetsPath = file.path(path.package("tempoR"),"dflatExample.gmt")
exampleGeneSets = loadGMT(exampleGeneSetsPath)
# }