Included EBSeq for downstream differential expression analysis

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

diff --git a/EBSeq/R/GetData.R b/EBSeq/R/GetData.R
new file mode 100644 (file)
index 0000000..ddccf38
--- /dev/null
+++ b/EBSeq/R/GetData.R
@@ -0,0 +1,35 @@
+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
+}
+