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

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

diff --git a/EBSeq/R/MergeIso.R b/EBSeq/R/MergeIso.R
deleted file mode 100644 (file)
index 50a0784..0000000
--- a/EBSeq/R/MergeIso.R
+++ /dev/null
@@ -1,103 +0,0 @@
-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)
-
-
-}
-