prepare4GSEA {InPAS} | R Documentation |
output the log2 transformed delta PDUI txt file and chip file for GSEA analysis
prepare4GSEA(eset, groupList, Preranked=TRUE, folder=".", rnkFilename="InPAS.rnk", chipFilename="InPAS.chip", dataFilename="dPDUI.txt", PhenFilename="group.cls")
eset |
a UTR3eSet object |
groupList |
group list of tag names |
Preranked |
logical value, out preranked or not |
folder |
output folder |
rnkFilename |
filename of preranked file |
chipFilename |
filename of chip |
dataFilename |
filename of dataset |
PhenFilename |
filename of Phenotype labels |
None
Jianhong Ou
file <- system.file("extdata", "eset.MAQC.rda", package="InPAS") load(file) gp1=c("Brain.auto", "Brain.phiX") gp2=c("UHR.auto", "UHR.phiX") groupList <- list(Brain=gp1, UHR=gp2) prepare4GSEA(eset, groupList=groupList, Preranked=FALSE)