changed output format to contain FPKM etc. ; fixed a bug for paired-end reads

[rsem.git] / EBSeq / R / PoolMatrix.R

diff --git a/EBSeq/R/PoolMatrix.R b/EBSeq/R/PoolMatrix.R
deleted file mode 100644 (file)
index 4c80785..0000000
--- a/EBSeq/R/PoolMatrix.R
+++ /dev/null
@@ -1,25 +0,0 @@
-PoolMatrix <-
-function(Data,reads,type)
-{
-poolnames=names(Data)
-poolM=NULL
-for (po in 1:8)
-       poolM=cbind(poolM,Data[[po]][,1])
-rownames(poolM)=rownames(Data[[1]])
-colnames(poolM)=poolnames
-
-#poolValue=poolM*reads
-poolValue=poolM
-for (col in 1:8)
-       poolValue[,col]=poolM[,col]*reads[col]
-poolValue=round(poolValue)
-if (type=="G")
-       {
-               poolM=cbind(Data[[1]][,2],poolM)
-               poolValue=cbind(Data[[1]][,2],poolValue)
-               colnames(poolM)=c("Groups",poolnames)
-               colnames(poolValue)=c("Groups",poolnames)
-       }
-poolOutput=list(poolM=poolM,poolValue=poolValue)
-}
-