--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/EBGeneTwoCondTest.R	Mon Jun 16 16:22:44 2014 -0400
@@ -0,0 +1,78 @@
+sink(file="/tmp/none")
+sink("/dev/null")
+options(warn=-1)
+options(echo=F) 
+
+invisible("EBSeq")
+suppressMessages(library("EBSeq"))
+
+args <- commandArgs(trailingOnly = T)
+inputfile <- args[1]
+WhetherSampleName <- args[2]
+CondIn <- args[3]
+FDR <- args[4]
+outputfile <- args[5]
+Sort.out<-args[6]
+Sort.out.FDR <-args[7]
+Sizesout <-args[8]
+
+Conditions=strsplit(CondIn,split=",")[[1]]
+
+if(WhetherSampleName=="y"){
+	ReadIn=read.table(inputfile,stringsAsFactors=F,header=T,sep="\t")
+	Names=names(ReadIn)[-1]
+	}
+if(WhetherSampleName=="n"){
+	ReadIn=read.table(inputfile,stringsAsFactors=F,header=F,sep="\t")
+	Names=paste0("S",1:length(Conditions))
+}
+
+if(class(ReadIn[[1]])=="character"){
+	GeneMat=do.call(cbind,ReadIn[-1])
+	rownames(GeneMat)=ReadIn[[1]]
+	colnames(GeneMat)=Names
+}
+if(class(ReadIn[[1]])=="numeric"){
+	GeneMat=data.matrix(ReadIn)
+	colnames(GeneMat)=Names
+	}
+
+
+Sizes=MedianNorm(GeneMat)
+EBOut=EBTest(Data=GeneMat,Conditions=as.factor(Conditions),sizeFactors=Sizes, maxround=5)
+PP=GetPP(EBOut)
+PP.sort=sort(PP,decreasing=T)
+PP.sort.FDR=PP.sort[which(PP.sort>=1-as.numeric(FDR))]
+
+Data.norm=GetNormalizedMat(GeneMat, Sizes)
+FC=PostFC(EBOut)
+realFC=FC[[2]]
+postFC=FC[[1]]
+
+Mat=cbind(PP, realFC[names(PP)], postFC[names(PP)],Data.norm[names(PP),])
+Mat.sort=cbind(PP.sort, realFC[names(PP.sort)], postFC[names(PP.sort)],Data.norm[names(PP.sort),])
+
+
+if(length(PP.sort.FDR)>1)Mat.sort.FDR=cbind(PP.sort.FDR, realFC[names(PP.sort.FDR)], postFC[names(PP.sort.FDR)],Data.norm[names(PP.sort.FDR),])
+
+if(length(PP.sort.FDR)==1)Mat.sort.FDR=matrix(
+		    c(PP.sort.FDR, realFC[names(PP.sort.FDR)], postFC[names(PP.sort.FDR)],Data.norm[names(PP.sort.FDR),])
+				    ,nrow=1)
+
+colnames(Mat)=colnames(Mat.sort)=
+					  c("PPDE","RealFC","PosteriorFC",colnames(Data.norm))
+if(length(PP.sort.FDR)>0)colnames(Mat.sort.FDR)=
+			      c("PPDE","RealFC","PosteriorFC",colnames(Data.norm))
+
+##cms - col.names changed below to have a header for the row names. This way the output of RSEM can be joined with EBSeq output
+#write.table(round(Mat,2),file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
+#write.table(round(Mat,2),file=outputfile,quote=F,col.names=NA,row.names=T,sep = "\t")  ##cms - made correction on 11/11/13
+write.table(round(Mat,2),file=outputfile,quote=F,col.names=c("gene_id\tPPDE","RealFC","PosteriorFC",colnames(Data.norm)),row.names=T,sep = "\t")  ##cms - made correction on 11/11/13
+#write.table(round(Mat.sort,2),file=Sort.out ,quote=F,col.names=T,row.names=T,sep = "\t")
+#write.table(round(Mat.sort,2),file=Sort.out ,quote=F,col.names=NA,row.names=T,sep = "\t")  ##cms - made correction on 11/11/13
+write.table(round(Mat.sort,2),file=Sort.out ,quote=F,col.names=c("gene_id\tPPDE","RealFC","PosteriorFC",colnames(Data.norm)),row.names=T,sep = "\t")  ##cms - made correction on 11/11/13
+#if(length(PP.sort.FDR)>0)write.table(round(Mat.sort.FDR,2),file=Sort.out.FDR,quote=F,col.names=T,row.names=T,sep = "\t")
+#if(length(PP.sort.FDR)>0)write.table(round(Mat.sort.FDR,2),file=Sort.out.FDR,quote=F,col.names=NA,row.names=T,sep = "\t")  ##cms - made correction on 11/11/13
+if(length(PP.sort.FDR)>0)write.table(round(Mat.sort.FDR,2),file=Sort.out.FDR,quote=F,col.names=c("gene_id\tPPDE","RealFC","PosteriorFC",colnames(Data.norm)),row.names=T,sep = "\t")  ##cms - made correction on 12/17/13; this preserves the header if merged with RSEM output.
+write.table(Sizes,file=Sizesout,quote=F,col.names=F,row.names=F,sep = "\t")
+