readGmt: readGmt

In PGSEA: Parametric Gene Set Enrichment Analysis

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 <[e-mail]>

References

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

See Also

writeGmt

Examples

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

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