normzalition

codescript/EPIC.raw.R

@@ -47,6 +47,12 @@ raw_mVals <- getM(mSetRaw)
 raw_bVals <- getBeta(mSetRaw)
 message("m value and beta value output:finished")
 
+# normalization
+MSet.noob <- preprocessNoob(rgSet)
+RSet <- ratioConvert(MSet.noob, what = "both", keepCN = TRUE)
+bVals <- getBeta(RSet)
+mVals <- getM(RSet)
+
 # write output
 message("saving R data")
 rdata_filename = paste(opt$prefix, '.RData',sep="")
@@ -56,3 +62,8 @@ m_raw_filename = paste(opt$prefix,'.raw.mVal.txt',sep="")
 write.table(raw_mVals,m_raw_filename,col.names = T,row.names = T,sep="\t",quote=F)
 b_raw_filename = paste(opt$prefix,'.raw.bVal.txt',sep="")
 write.table(raw_bVals,b_raw_filename,col.names = T,row.names = T,sep="\t",quote=F)
+message("writing filtered table")
+m_filename = paste(opt$prefix,'.ssnoob.mVal.txt',sep="")
+write.table(mVals,m_filename,col.names = T,row.names = T,sep="\t",quote=F)
+b_filename = paste(opt$prefix,'.ssnoob.bVal.txt',sep="")
+write.table(bVals,b_filename,col.names = T,row.names = T,sep="\t",quote=F)

tasks/minfi.wdl

@@ -22,5 +22,7 @@ task minfi {
 		  File rdata = "${prefix}.RData"
       File raw_mVal = "${prefix}.raw.mVal.txt"
       File raw_bVal = "${prefix}.raw.bVal.txt"
+      File normed_mVal = "${prefix}.ssnoob.mVal.txt"
+      File normed_bVal = "${prefix}.ssnoob.bVal.txt"
     }
   }