readGmt {PGSEA} | R Documentation

## readGmt

### Description

This function will read a "gmt" file into R, returning results as a list of SMC objects.

### Usage

    readGmt(fname)

### Arguments

`fname` | File name of concepts in .gmt format

### 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.

### Value

A list of SMC objects

### Author(s)

Karl Dykema <karl.dykema@vai.org>

### References

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

### See Also

`writeGmt`

### Examples

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

[Package PGSEA version 1.2.0 Index]