writeGmt {PGSEA} | R Documentation

## writeGmt

### 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 <kyle.furge@vai.org> and Karl Dykema <karl.dykema@vai.org>

### 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)

[Package PGSEA version 1.56.0 Index]