geneSignatureFinder (version 2014.02.17)

puttingAllTogether: Example of strategy to find signature from different seeds at the same time and to generate plots and summary table.

Description

This function has been designed to show how to put the functions of the package in sequence in order to analyse microarray data for signatures. Given this function is an example, and can be run for small microarray data, the user is invited to a reverse engineering task (start by typing "puttingAllTogether") in order to define a procedure for more complex analysis sessions.

Usage

puttingAllTogether(workingFile = "", nchips = 2, alpha = 0.05, saveSurvivalCurvesPlot = FALSE, saveIndividualSignature = FALSE,  saveImportancePlot = FALSE)

Arguments

workingFile

prefix string for the log file and other output

nchips

see the NCPUS() function for details; it has to be set to the number of cpu's to use if useCpuCluster = TRUE

alpha

see the BHcorrection() function

saveSurvivalCurvesPlot

if TRUE a plot of the two survival curves of the signature are stored in a .pdf file in the working directory

saveIndividualSignature

if TRUE a .RData file is stored in the working directory with the result of the signatureFinder() function

saveImportancePlot

if TRUE a plot of the importances of the genes in the signature are stored in a .pdf file in the working directory

Value

Details

The plotting of the figures may not work if a graphical device is not instantiated.

Examples

get("puttingAllTogether")

# uncomment the following lines to performe an analysis
# of the non small cells lung cancer (NSCLC) data 

##################
#data(geNSCLC)
#geData <- geNSCLC
#data(stNSCLC)
#stData <- stNSCLC

#puttingAllTogether(
#	workingFile = "NSCLC",
######### modify the number of cpu according to your machine
#	nchips = 2,
#	saveIndividualSignature = TRUE)