Gene Signature Finder
Gene Signature Finder (GSF) is an R package devoted to discovering prognostic gene-signatures with the aid of survival time data.
The packackage can be either downloaded from CRAN at this link, or installed in R with this command
For a quick run of the procedure execute the commands
library("geneSignatureFinder") data(geNSCLC) geData <- geNSCLC data(stNSCLC) stData <- stNSCLC
The code you are going to run generates some tabular output that can be stored as .xls file if the library WriteXLS is installed on your system. Otherwise the tabular results are displayed on thye screen.
The searching procedures are written so that the processes can be distributed on different CPU. To speedup the run check how many CPU's are on your system and tune the nchips parameter according to this number.
puttingAllTogether( workingFile = "NSCLC", ######### modify the number of cpu according to your machine nchips = 2, useCpuCluster = TRUE, saveIndividualSignature = TRUE)