'rsem-run-ebseq': Added 'output_file.condmeans' for tests with more than 2 conditions

[rsem.git] / EBSeq / rsem-for-ebseq-find-DE

diff --git a/EBSeq/rsem-for-ebseq-find-DE b/EBSeq/rsem-for-ebseq-find-DE
index 07b989991cea46e63d064eacaa475c3731227398..3c5d304d6ca5bb250789c3ac50b904a686fcde9a 100755 (executable)
--- a/EBSeq/rsem-for-ebseq-find-DE
+++ b/EBSeq/rsem-for-ebseq-find-DE
@@ -58,8 +58,12 @@ if (nc == 2) {
 
   results <- cbind(PP, MultiPP$MAP[rownames(PP)], probs)
   colnames(results) <- c(colnames(PP), "MAP", "PPDE")  
-  results <- results[order(results[,"PPDE"], decreasing = TRUE),]
+  ord <- order(results[,"PPDE"], decreasing = TRUE)
+  results <- results[ord,]
   write.table(results, file = output_file, sep = "\t")
 
   write.table(MultiPP$Patterns, file = paste(output_file, ".pattern", sep = ""), sep = "\t")
+
+  MultiFC <- GetMultiFC(MultiOut)
+  write.table(MultiFC$CondMeans[ord,], file = paste(output_file, ".condmeans", sep = ""), sep = "\t")
 }