parseGMT {EnrichmentBrowser} | R Documentation |
Functionaliy for parsing and writing a list of gene sets from/to a flat text file in GMT format.
writeGMT( gs, gmt.file ) parse.genesets.from.GMT( gmt.file )
gs |
A list of gene sets (character vectors of gene IDs). |
gmt.file |
Gene set file in GMT format. See 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.
For parse.genesets.from.GMT
: a list of gene sets (vectors of gene IDs).
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
GMT file format http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats
# 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)