writeGmt: writeGmt

In PGSEA: Parametric Gene Set Enrichment Analysis

Description

This function writes out SMC objects into .gmt file format

Usage

writeGmt(fname, cl)

Arguments

fname	name of the file to be written out
cl	list of SMC objects

Details

The .gmt file format is a tab delimited file format used to store gene lists. These gene lists are stored row by row. The first column is the gene set name. The second column is a brief description, and every entry after that is a gene within that gene set.

Author(s)

Kyle Furge <[e-mail]> and Karl Dykema <[e-mail]>

References

http://www.broad.mit.edu/gsea/doc/data_formats.html#gmt

See Also

readGmt

Examples

	datadir <- system.file("extdata", package = "PGSEA")
	sample <- readGmt(file.path(datadir, "sample.gmt"))
	str(sample)

## Not run: 
	writeGmt(paste(datadir,"/output.gmt",sep=""),sample)

## End(Not run)

PGSEA documentation built on April 28, 2020, 8:28 p.m.