writeGmt: writeGmt

Description Usage Arguments Details Author(s) References See Also Examples

View source: R/PGSEA.R

Description

This function writes out SMC objects into .gmt file format

Usage

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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 <[email protected]> and Karl Dykema <[email protected]>

References

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

See Also

readGmt

Examples

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	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 Nov. 1, 2018, 3:36 a.m.