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

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

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)

Example output

Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: limma
Loading required package: biomaRt
Loading required package: iC10
Loading required package: pamr
Loading required package: cluster
Loading required package: impute
Loading required package: iC10TrainingData
Loading required package: AIMS
Loading required package: e1071
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:limma':

    plotMA

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

List of 7
 $ ESR1 :'data.frame':	469 obs. of  6 variables:
 $ ERBB2:'data.frame':	28 obs. of  6 variables:
 $ AURKA:'data.frame':	229 obs. of  6 variables:
 $ PLAU :'data.frame':	68 obs. of  6 variables:
 $ VEGF :'data.frame':	14 obs. of  6 variables:
 $ STAT1:'data.frame':	95 obs. of  6 variables:
 $ CASP3:'data.frame':	10 obs. of  6 variables:
List of 3
 $ GENIUSM1:'data.frame':	63 obs. of  5 variables:
 $ GENIUSM2:'data.frame':	22 obs. of  5 variables:
 $ GENIUSM3:'data.frame':	229 obs. of  5 variables:

genefu documentation built on Jan. 28, 2021, 2:01 a.m.