read.m.file: Function to read a 'csv' file containing gene lists (aka gene...

In bhklab/genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

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.

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)

bhklab/genefu documentation built on Nov. 30, 2024, 9:03 p.m.