Included EBSeq for downstream differential expression analysis

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

diff --git a/EBSeq/R/MergeIso.R b/EBSeq/R/MergeIso.R
new file mode 100644 (file)
index 0000000..50a0784
--- /dev/null
+++ b/EBSeq/R/MergeIso.R
@@ -0,0 +1,103 @@
+MergeIso <-
+function(IsoSIMout, Num, Path="./"){
+NumSample=ncol(do.call(rbind, IsoSIMout[[i]]$generateData))
+
+NumIso=rep(0,Num)
+for (i in 1:Num)NumIso[i]=nrow(do.call(rbind, IsoSIMout[[i]]$generateData))
+
+MinNumIso=min(NumIso)
+AproxNumDE=length(unlist(IsoSIMout[[1]]$TrueDE))
+       
+IsoMergeTable=matrix(rep(0,60),nrow=10)
+       for(i in 1:Num)IsoMergeTable=IsoMergeTable+IsoSIMout[[i]][[1]]
+       IsoMergeTable=IsoMergeTable/Num
+       IsoMergeTable=round(IsoMergeTable,2)
+                 
+       IsoMergeDVD=rep(0,2)
+         for(i in 1:Num)IsoMergeDVD=IsoMergeDVD+IsoSIMout[[i]][[3]]
+                 IsoMergeDVD=round(IsoMergeDVD/Num,2) 
+                                         
+         IsoMergePhi=matrix(rep(0,18),nrow=2)
+                 for(i in 1:Num)IsoMergePhi=IsoMergePhi+IsoSIMout[[i]][[4]]
+                         IsoMergePhi=round(IsoMergePhi/Num,2)
+## Write
+TXTname=paste(paste("../IsoOutput/",paste("Iso","DVD",IsoMergeDVD[1], IsoMergeDVD[2],"Sample",NumSample,sep="_"),sep=""),".txt",sep="")
+write.table(IsoMergeTable, file=TXTname)
+
+
+####### Note everytime # DE genes and # total genes may different. (since NA issue)
+  IsoMergeFD=matrix(rep(0,5*MinNumIso),ncol=5)
+  IsoMergeFD.p=matrix(rep(0,5*MinNumIso),ncol=5)
+  IsoMergeTP.p=matrix(rep(0,5*MinNumIso),ncol=5)
+  IsoMergeFN.p=matrix(rep(0,5*MinNumIso),ncol=5)
+  IsoMergeTN.p=matrix(rep(0,5*MinNumIso),ncol=5)
+  IsoMergeFDR=matrix(rep(0,5*MinNumIso),ncol=5)
+  IsoMergeTPR=matrix(rep(0,5*MinNumIso),ncol=5)
+  IsoMergeFPR=matrix(rep(0,5*MinNumIso),ncol=5)
+
+  for(i in 1:Num){
+       # Make sure names in the same order
+       # Get FD number for each number of genes found
+       # columns are samples 
+    TotalNum=nrow(do.call(rbind, IsoSIMout[[i]]$generateData))
+       NumDE=length(unlist(IsoSIMout[[i]]$TrueDE))
+       EBSeqNames=names(IsoSIMout[[i]]$EBSeqPP)
+    tmpMatrix=cbind(IsoSIMout[[i]]$DESeqP[EBSeqNames],IsoSIMout[[i]]$edgeRP[EBSeqNames], exp(IsoSIMout[[i]]$BaySeqPP[EBSeqNames,2]),IsoSIMout[[i]]$BBSeqP[EBSeqNames],IsoSIMout[[i]]$EBSeqPP)
+       # Bayseq and EBseq are PP. Others are p value 
+    tmpFD=TopCts(tmpMatrix, c(0,0,1,0,1), unlist(IsoSIMout[[i]]$TrueDE)[unlist(IsoSIMout[[i]]$TrueDE)%in%EBSeqNames], MinNumIso)
+    # Get percentage for FP, TP, TN, FN!
+       tmpFD.p=tmpFD/TotalNum
+       # TP = Find - FD
+       tmpTP.p=(outer(c(1:MinNumIso),rep(1,5))-tmpFD)/TotalNum
+       # FN = TrueDE - TP
+       tmpFN.p=NumDE/TotalNum - tmpTP.p
+       # TN = TrueEE - FD
+       tmpTN.p=(TotalNum-NumDE)/TotalNum - tmpFD.p
+       
+       tmpFDR=tmpFD.p/(tmpFD.p+tmpTP.p)
+       tmpFPR=tmpFD.p/(tmpFD.p+tmpTN.p)
+       tmpTPR=tmpTP.p/(tmpFN.p+tmpTP.p)
+       IsoMergeFDR=IsoMergeFDR+tmpFDR
+       IsoMergeTPR=IsoMergeTPR+tmpTPR
+       IsoMergeFPR=IsoMergeFPR+tmpFPR
+
+    IsoMergeFD.p=IsoMergeFD.p+tmpFD.p
+       IsoMergeTP.p=IsoMergeTP.p+tmpTP.p
+       IsoMergeFN.p=IsoMergeFN.p+tmpFN.p
+       IsoMergeTN.p=IsoMergeTN.p+tmpTN.p
+
+       IsoMergeFD=IsoMergeFD+tmpFD
+ }   
+  IsoMergeFD=IsoMergeFD/Num
+  IsoMergeFD.p=IsoMergeFD.p/Num
+  IsoMergeTP.p=IsoMergeTP.p/Num
+  IsoMergeFN.p=IsoMergeFN.p/Num
+  IsoMergeTN.p=IsoMergeTN.p/Num
+  IsoMergeFDR=IsoMergeFDR/Num
+  IsoMergeTPR=IsoMergeTPR/Num
+  IsoMergeFPR=IsoMergeFPR/Num
+
+PlotTopName=paste(paste(Path,paste("Top","Iso","DVD",IsoMergeDVD[1], IsoMergeDVD[2],"Sample",NumSample, sep="_"),sep=""),".pdf",sep="")
+
+TrueDELength=length(unlist(IsoSIMout[[i]]$TrueDE)[unlist(IsoSIMout[[i]]$TrueDE)%in%EBSeqNames])
+pdf(PlotTopName)
+  PlotTopCts(TrueDELength,IsoMergeFD[1:TrueDELength,],c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
+dev.off()
+
+
+PlotFDName=paste(paste(Path,paste("FDTP","Iso","DVD",IsoMergeDVD[1], IsoMergeDVD[2],"Sample",NumSample,sep="_"),sep=""),".pdf",sep="")
+pdf(PlotFDName)
+  PlotFDTP(MinNumIso,IsoMergeFDR, IsoMergeTPR, c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
+dev.off()
+
+PlotFPName=paste(paste(Path,paste("FPRTP","Iso","DVD",IsoMergeDVD[1], IsoMergeDVD[2],"Sample",NumSample,sep="_"),sep=""),".pdf",sep="")
+pdf(PlotFPName)
+  PlotFPTP(MinNumIso,IsoMergeFPR, IsoMergeTPR, c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
+  dev.off()
+
+
+out=list(IsoMergeTable=IsoMergeTable, IsoMergeDVD=IsoMergeDVD, IsoMergePhi=IsoMergePhi, IsoMergeFD=IsoMergeFD)
+
+
+}
+