gsaReadGmt: Read in a gene set collection from a .gmt file

In bernau/survHDExtra: Addtitional Features for package survHD

Description

Read in a gene set collection from a .gmt file. Code was adapted from the GSA package by Tibshirani and Efron.

Usage

    gsaReadGmt(filename, direction)

Arguments

filename	The name of a file to read data values from. Should be a tab-separated text file, with one row per gene set. Column 1 has gene set names (identifiers), column 2 has gene set descriptions, remaining columns are gene ids for genes in that geneset.
direction	Optionally, if the gene set consists of only up- or down-regulated genes, this direction ("up" or "down").

Details

Reads gene sets in the GMT format, for example from MSigDB.

Value

An object of class gsagenesets.

Author(s)

Robert Tibshirani (adapted from the GSA package), Markus Riester [e-mail], Levi Waldron [e-mail], Christoph Bernau [e-mail]

See Also

gsaWilcoxSurv

Examples

    require(survHD)
    require(survHDExtra)
    gmt <- gsaReadGmt(system.file("extdata/ovarian_gene_signatures.gmt",
    package = "survHD"))

bernau/survHDExtra documentation built on May 12, 2019, 4:22 p.m.