#for required R library
install.packages("preprocessCore")
install.packages("MASS")
#quick start Please, download the code and unzip the folder. (make sure to unzip the folder bgDistribution)
Execute R and set the working directory to the unzipped folder of downloaded codes.
Run the following codes.
#Run using precalculated background distribution
tumorFile = "Beer_10samples.txt"
refFile = "LUAD_nREF.txt"
pathwayListFile= "reactome.txt"
whoami = "testRun2"
runMode = "nRef"
sourcePath = "iPAS_library.r"
source(sourcePath)
bgDistributionPath = "./bgDistribution"
iPAS( tumorFile, refFile, pathwayListFile, whoami, runMode, bgDistributionPath ) #Run without using precalculated background distribution
#This is slower because it generate background distribution for p-values
#Note the argument ‘bgDistributionPath’ is blank for this run
tumorFile = "Beer_10samples.txt"
refFile = "LUAD_nREF.txt"
pathwayListFile= "reactome.txt"
whoami = "testRun2"
runMode = "nRef"
sourcePath = "iPAS_library.r"
source(sourcePath )
bgDistributionPath = ""
iPAS( tumorFile, refFile, pathwayListFile, whoami, runMode, bgDistributionPath )
Total running time of this test code is approximately 30-45 mins (for 583 pathways, 10 samples).
#nRef files
colon mucosa normal tissues (zipped)
contact: taejin.ahn@gmail.com