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 1.10.0 Index]