parseGMT {EnrichmentBrowser}R Documentation

Reading from and writing to GMT file format for gene sets

Description

Functionaliy for parsing and writing a list of gene sets from/to a flat text file in GMT format.

Usage

    writeGMT( gs, gmt.file )

    parse.genesets.from.GMT( gmt.file )

Arguments

gs

A list of gene sets (character vectors of gene IDs).

gmt.file

Gene set file in GMT format. See details.

Details

The GMT (Gene Matrix Transposed) file format is a tab delimited file format that describes gene sets. In the GMT format, each row represents a gene set. Each gene set is described by a name, a description, and the genes in the gene set. See references.

Value

For parse.genesets.from.GMT: a list of gene sets (vectors of gene IDs).

Author(s)

Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>

References

GMT file format http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

Examples

    # parsing gene sets from GMT
    gmt.file <- system.file("extdata/hsa_kegg_gs.gmt", package="EnrichmentBrowser")
    gs <- parse.genesets.from.GMT(gmt.file)     
    
    # writing gene sets to file
    writeGMT(gs, gmt.file)

[Package EnrichmentBrowser version 2.8.7 Index]