Included EBSeq for downstream differential expression analysis

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

diff --git a/EBSeq/R/MergeGene.R b/EBSeq/R/MergeGene.R
new file mode 100644 (file)
index 0000000..4bfdaf4
--- /dev/null
+++ b/EBSeq/R/MergeGene.R
@@ -0,0 +1,107 @@
+MergeGene <-
+function(GeneSIMout, Num, Path="./"){
+NumSample=ncol(GeneSIMout[[i]]$generateData)
+
+NumGene=rep(0,Num)
+for (i in 1:Num)NumGene[i]=nrow(GeneSIMout[[i]]$generateData)
+
+MinNumGene=min(NumGene)
+AproxNumDE=length(GeneSIMout[[1]]$TrueDE)
+       
+GeneMergeTable=matrix(rep(0,12),nrow=6)
+       for(i in 1:Num)GeneMergeTable=GeneMergeTable+GeneSIMout[[i]][[1]]
+       GeneMergeTable=GeneMergeTable/Num
+       GeneMergeTable=round(GeneMergeTable,2)
+                 
+       GeneMergeDVD=rep(0,2)
+         for(i in 1:Num)GeneMergeDVD=GeneMergeDVD+GeneSIMout[[i]][[3]]
+                 GeneMergeDVD=round(GeneMergeDVD/Num,2) 
+                                         
+         GeneMergePhi=matrix(rep(0,2),nrow=2)
+                 for(i in 1:Num)GeneMergePhi=GeneMergePhi+GeneSIMout[[i]][[4]]
+                         GeneMergePhi=round(GeneMergePhi/Num,2)
+## Write
+TXTname=paste(paste(Path,paste("Gene","DVD",GeneMergeDVD[1], GeneMergeDVD[2],"Phi",GeneMergePhi[1], GeneMergePhi[2],"Sample",NumSample,sep="_"),sep=""),".txt",sep="")
+write.table(GeneMergeTable, file=TXTname)
+
+
+####### Note everytime # DE genes and # total genes may different. (since NA issue)
+  GeneMergeFD=matrix(rep(0,5*MinNumGene),ncol=5)
+  GeneMergeFD.p=matrix(rep(0,5*MinNumGene),ncol=5)
+  GeneMergeTP.p=matrix(rep(0,5*MinNumGene),ncol=5)
+  GeneMergeFN.p=matrix(rep(0,5*MinNumGene),ncol=5)
+  GeneMergeTN.p=matrix(rep(0,5*MinNumGene),ncol=5)
+
+  GeneMergeFDR=matrix(rep(0,5*MinNumGene),ncol=5)
+  GeneMergeTPR=matrix(rep(0,5*MinNumGene),ncol=5)
+  GeneMergeFPR=matrix(rep(0,5*MinNumGene),ncol=5)
+
+
+  for(i in 1:Num){
+       # Make sure names in the same order
+       # Get FD number for each number of genes found
+    TotalNum=nrow(GeneSIMout[[i]]$generateData)
+       NumDE=length(GeneSIMout[[i]]$TrueDE)
+       EBSeqNames=names(GeneSIMout[[i]]$EBSeqPP)
+    tmpMatrix=cbind(GeneSIMout[[i]]$DESeqP[EBSeqNames],GeneSIMout[[i]]$edgeRP[EBSeqNames], exp(GeneSIMout[[i]]$BaySeqPP[EBSeqNames,2]),GeneSIMout[[i]]$BBSeqP[EBSeqNames],GeneSIMout[[i]]$EBSeqPP)
+       # Bayseq and EBseq are PP. Others are p value 
+    tmpFD=TopCts(tmpMatrix, c(0,0,1,0,1), GeneSIMout[[i]]$TrueDE[GeneSIMout[[i]]$TrueDE%in%EBSeqNames], MinNumGene)
+    # Get percentage for FP, TP, TN, FN!
+       tmpFD.p=tmpFD/TotalNum
+       # TP = Find - FD
+       tmpTP.p=(c(1:MinNumGene)-tmpFD)/TotalNum
+       # FN = TrueDE - TP
+       tmpFN.p=NumDE/TotalNum - tmpTP.p
+       # TN = TrueEE - FD
+       tmpTN.p=(TotalNum-NumDE)/TotalNum - tmpFD.p
+       
+       
+       tmpFDR=tmpFD.p/(tmpFD.p+tmpTP.p)
+       tmpFPR=tmpFD.p/(tmpFD.p+tmpTN.p)
+       tmpTPR=tmpTP.p/(tmpFN.p+tmpTP.p)
+       GeneMergeFDR=GeneMergeFDR+tmpFDR
+       GeneMergeTPR=GeneMergeTPR+tmpTPR
+       GeneMergeFPR=GeneMergeFPR+tmpFPR
+
+    GeneMergeFD.p=GeneMergeFD.p+tmpFD.p
+       GeneMergeTP.p=GeneMergeTP.p+tmpTP.p
+       GeneMergeFN.p=GeneMergeFN.p+tmpFN.p
+       GeneMergeTN.p=GeneMergeTN.p+tmpTN.p
+
+       GeneMergeFD=GeneMergeFD+tmpFD
+ }   
+  GeneMergeFD=GeneMergeFD/Num
+  GeneMergeFD.p=GeneMergeFD.p/Num
+  GeneMergeTP.p=GeneMergeTP.p/Num
+  GeneMergeFN.p=GeneMergeFN.p/Num
+  GeneMergeTN.p=GeneMergeTN.p/Num
+
+  GeneMergeFDR=GeneMergeFDR/Num
+  GeneMergeTPR=GeneMergeTPR/Num
+  GeneMergeFPR=GeneMergeFPR/Num
+
+
+PlotTopName=paste(paste(Path,paste("Top","Gene","DVD",GeneMergeDVD[1], GeneMergeDVD[2],"Phi",GeneMergePhi[1], GeneMergePhi[2],"Sample",NumSample, sep="_"),sep=""),".pdf",sep="")
+
+TrueDELength=length(GeneSIMout[[i]]$TrueDE[GeneSIMout[[i]]$TrueDE%in%EBSeqNames])
+pdf(PlotTopName)
+  PlotTopCts(TrueDELength,GeneMergeFD[1:TrueDELength,],c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
+dev.off()
+
+
+PlotFDName=paste(paste(Path,paste("FDTP","Gene","DVD",GeneMergeDVD[1], GeneMergeDVD[2],"Phi",GeneMergePhi[1], GeneMergePhi[2],"Sample",NumSample,sep="_"),sep=""),".pdf",sep="")
+pdf(PlotFDName)
+  PlotFDTP(MinNumGene,GeneMergeFDR, GeneMergeTPR, c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
+dev.off()
+
+PlotFPName=paste(paste(Path,paste("FPRTP","Gene","DVD",GeneMergeDVD[1], GeneMergeDVD[2],"Phi",GeneMergePhi[1], GeneMergePhi[2],"Sample",NumSample,sep="_"),sep=""),".pdf",sep="")
+pdf(PlotFPName)
+  PlotFPTP(MinNumGene,GeneMergeFPR, GeneMergeTPR, c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
+  dev.off()
+
+
+out=list(GeneMergeTable=GeneMergeTable, GeneMergeDVD=GeneMergeDVD, GeneMergePhi=GeneMergePhi, GeneMergeFD=GeneMergeFD)
+
+
+}
+