From f4cf635eec30c7bcadb40d176a05c240266df81a Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Tue, 22 Jul 2014 16:45:00 +0200
Subject: [PATCH] cont. cummerbund methods
---
R/bio/cummerutils.R | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/R/bio/cummerutils.R b/R/bio/cummerutils.R
index ed55dd2..6522de5 100644
--- a/R/bio/cummerutils.R
+++ b/R/bio/cummerutils.R
@@ -1,14 +1,18 @@
-require.auto(cummeRbund)
+require(cummeRbund)
-
-getExpressedGenes <- function(cuff, minFPKM=1, logMode=F){
+getExpressedGenes <- function(cuff, ...){
fpkmMat<-repFpkmMatrix(genes(cuff))
+ rownames(filterByExpression(fpkmMat, ...))
+}
+
+
+filterByExpression <- function(fpkmMat, minFPKM=1, logMode=F){
if(logMode) fpkmMat<-log10(fpkmMat+1) ## add a pseudocount
geneMax <- apply(fpkmMat, 1, max)
- rownames(fpkmMat[geneMax>minFPKM,])
+ fpkmMat[geneMax>minFPKM,]
}
--
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