read.m.file {genefu} | R Documentation

## Function to read a 'csv' file containing gene lists (aka gene signatures)

### Description

This function allows for reading a 'csv' file containing gene signatures. Each gene signature is composed of at least four columns: "gene.list" is the name of the signature on the first line and empty fields below, "probes" are the probe names, "EntrezGene.ID" are the EntrezGene IDs and "coefficient" are the coefficients of each probe.

### Usage

    read.m.file(file, ...)

### Arguments

`file` | Filename of the 'csv' file.
`...` | Additional parameters for `read.csv` function.

### Value

List of gene signatures.

### Author(s)

Benjamin Haibe-Kains

### See Also

`mod1`, `mod2`, 'extdata/desmedt2008_genemodules.csv', 'extdata/haibekains2009_sig_genius.csv'

### Examples

    ## read the seven gene modules as published in Desmedt et al 2008
    genemods <- read.m.file(system.file("extdata/desmedt2008_genemodules.csv",
      package = "genefu"))
    str(genemods, max.level=1)
    ## read the three subtype signtaures from GENIUS
    geniusm <- read.m.file(system.file("extdata/haibekains2009_sig_genius.csv",
      package = "genefu"))
    str(geniusm, max.level=1)

[Package genefu version 2.20.0 Index]