Category: Microarray data analysis

#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

lung normal tissues (zipped)

colon mucosa normal tissues (zipped)

contact: taejin.ahn@gmail.com