Added qn.bmiq normalization

loosolab · Aug 31, 2016 · 22496b5 · 22496b5
1 parent e17e2c9
commit 22496b5
Showing 1 changed file with 12 additions and 0 deletions.
diff --git a/src/normalizeAndCreateTables.R b/src/normalizeAndCreateTables.R
@@ -49,3 +49,15 @@ if(normalization == "quantile") {
 	write.table(getM(mSet)[-failed_probes,], file = paste(targetDir, "mValues_quantile.txt", sep="/"), quote = F, sep = "\t", row.names = T, col.names = T)
 	write.table(getBeta(mSet)[-failed_probes,], file = paste(targetDir, "betaValues_qunatile.txt", sep="/"), quote = F, sep = "\t", row.names = T, col.names = T)
 }
+
+if(normalization == "qn.bmiq") {
+	mSet = preprocessQuantile(rgSet, fixOutliers=fixOutliers, removeBadSamples=removeBadSamples, badSampleCutoff=badSampleCutoff)
+	betas = getBeta(mSet)[-failed_probes,]
+	design = ifelse(rownames(betas) %in% getProbeInfo(rgSet, type="I")$Name, 1, 2)
+	bnorm = lapply(1:ncol(betas), function(i) BMIQ(betas[,i],design=design)$all)
+	betaValues = do.call("cbind", bnorm)
+	colnames(betaValues) = colnames(betas)
+	mValues = apply(betaValues, 2, logit2)
+	write.table(mValues, file=paste(targetDir, "mValues_qn.bmiq.txt", sep="/"), quote = F, sep = "\t", row.names = T, col.names = T)
+	write.table(betaValues, file=paste(targetDir, "betaValues_qn.bmiq.txt", sep="/"), quote = F, sep = "\t", row.names = T, col.names = T)
+}