From 4aadc438d9993235397bf55b11ee90c4e6a22872 Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Fri, 18 Jul 2014 12:50:17 +0200
Subject: [PATCH] fixed expression filter
---
R/bio/cummerutils.R | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/R/bio/cummerutils.R b/R/bio/cummerutils.R
index 32e18f2..dcba773 100644
--- a/R/bio/cummerutils.R
+++ b/R/bio/cummerutils.R
@@ -1,14 +1,14 @@
-
require.auto(cummeRbund)
+
getExpressedGenes <- function(cuff, minFPKM=1, logMode=F){
- fpkmMat<-repFpkmMatrix(genes(cuff))
+ fpkmMat<-repFpkmMatrix(genes(mmusCuff))
if(logMode) fpkmMat<-log10(fpkmMat+1) ## add a pseudocount
geneMax <- apply(fpkmMat, 1, max)
- fpkmMat[geneMax>minFPKM,]$gene_id
+ rownames(fpkmMat[geneMax>minFPKM,])
}
--
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