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

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

diff --git a/EBSeq/R/GetData.R b/EBSeq/R/GetData.R
deleted file mode 100644 (file)
index ddccf38..0000000
--- a/EBSeq/R/GetData.R
+++ /dev/null
@@ -1,35 +0,0 @@
-GetData <-
-function(path,Name1,Name2,type)
-{
-Data=vector("list",8)
-Filenames=NULL
-Tablenames=NULL
-for (name in 1:4)
-       {
-               if (type=="I")
-                       Filenames=c(Filenames,paste(path,Name1,name,"_isoform_nus.tab",sep=""))  
-               if (type=="G")  
-                       Filenames=c(Filenames,paste(path,Name1,name,"_gene_nus.tab",sep=""))  
-               Tablenames=c(Tablenames,paste(Name1,name,sep=""))
-       }
-for (name in 1:4)
-       {
-               if (type=="I")
-                       Filenames=c(Filenames,paste(path,Name2,name,"_isoform_nus.tab",sep=""))
-               if (type=="G")
-                       Filenames=c(Filenames,paste(path,Name2,name,"_gene_nus.tab",sep=""))
-               Tablenames=c(Tablenames,paste(Name2,name,sep=""))
-       }
-
-
-names(Data)=Tablenames
-for (file in 1:8)
-       {
-               temp=read.table(Filenames[file],header=T)
-               temp2=as.matrix(temp[-1])
-               rownames(temp2)=as.vector(as.matrix(temp[1]))
-               Data[[file]]=temp2
-       }
-       Data
-}
-