2 function(IsoSIMout, Num, Path="./"){
3 NumSample=ncol(do.call(rbind, IsoSIMout[[i]]$generateData))
6 for (i in 1:Num)NumIso[i]=nrow(do.call(rbind, IsoSIMout[[i]]$generateData))
9 AproxNumDE=length(unlist(IsoSIMout[[1]]$TrueDE))
11 IsoMergeTable=matrix(rep(0,60),nrow=10)
12 for(i in 1:Num)IsoMergeTable=IsoMergeTable+IsoSIMout[[i]][[1]]
13 IsoMergeTable=IsoMergeTable/Num
14 IsoMergeTable=round(IsoMergeTable,2)
17 for(i in 1:Num)IsoMergeDVD=IsoMergeDVD+IsoSIMout[[i]][[3]]
18 IsoMergeDVD=round(IsoMergeDVD/Num,2)
20 IsoMergePhi=matrix(rep(0,18),nrow=2)
21 for(i in 1:Num)IsoMergePhi=IsoMergePhi+IsoSIMout[[i]][[4]]
22 IsoMergePhi=round(IsoMergePhi/Num,2)
24 TXTname=paste(paste("../IsoOutput/",paste("Iso","DVD",IsoMergeDVD[1], IsoMergeDVD[2],"Sample",NumSample,sep="_"),sep=""),".txt",sep="")
25 write.table(IsoMergeTable, file=TXTname)
28 ####### Note everytime # DE genes and # total genes may different. (since NA issue)
29 IsoMergeFD=matrix(rep(0,5*MinNumIso),ncol=5)
30 IsoMergeFD.p=matrix(rep(0,5*MinNumIso),ncol=5)
31 IsoMergeTP.p=matrix(rep(0,5*MinNumIso),ncol=5)
32 IsoMergeFN.p=matrix(rep(0,5*MinNumIso),ncol=5)
33 IsoMergeTN.p=matrix(rep(0,5*MinNumIso),ncol=5)
34 IsoMergeFDR=matrix(rep(0,5*MinNumIso),ncol=5)
35 IsoMergeTPR=matrix(rep(0,5*MinNumIso),ncol=5)
36 IsoMergeFPR=matrix(rep(0,5*MinNumIso),ncol=5)
39 # Make sure names in the same order
40 # Get FD number for each number of genes found
42 TotalNum=nrow(do.call(rbind, IsoSIMout[[i]]$generateData))
43 NumDE=length(unlist(IsoSIMout[[i]]$TrueDE))
44 EBSeqNames=names(IsoSIMout[[i]]$EBSeqPP)
45 tmpMatrix=cbind(IsoSIMout[[i]]$DESeqP[EBSeqNames],IsoSIMout[[i]]$edgeRP[EBSeqNames], exp(IsoSIMout[[i]]$BaySeqPP[EBSeqNames,2]),IsoSIMout[[i]]$BBSeqP[EBSeqNames],IsoSIMout[[i]]$EBSeqPP)
46 # Bayseq and EBseq are PP. Others are p value
47 tmpFD=TopCts(tmpMatrix, c(0,0,1,0,1), unlist(IsoSIMout[[i]]$TrueDE)[unlist(IsoSIMout[[i]]$TrueDE)%in%EBSeqNames], MinNumIso)
48 # Get percentage for FP, TP, TN, FN!
49 tmpFD.p=tmpFD/TotalNum
51 tmpTP.p=(outer(c(1:MinNumIso),rep(1,5))-tmpFD)/TotalNum
53 tmpFN.p=NumDE/TotalNum - tmpTP.p
55 tmpTN.p=(TotalNum-NumDE)/TotalNum - tmpFD.p
57 tmpFDR=tmpFD.p/(tmpFD.p+tmpTP.p)
58 tmpFPR=tmpFD.p/(tmpFD.p+tmpTN.p)
59 tmpTPR=tmpTP.p/(tmpFN.p+tmpTP.p)
60 IsoMergeFDR=IsoMergeFDR+tmpFDR
61 IsoMergeTPR=IsoMergeTPR+tmpTPR
62 IsoMergeFPR=IsoMergeFPR+tmpFPR
64 IsoMergeFD.p=IsoMergeFD.p+tmpFD.p
65 IsoMergeTP.p=IsoMergeTP.p+tmpTP.p
66 IsoMergeFN.p=IsoMergeFN.p+tmpFN.p
67 IsoMergeTN.p=IsoMergeTN.p+tmpTN.p
69 IsoMergeFD=IsoMergeFD+tmpFD
71 IsoMergeFD=IsoMergeFD/Num
72 IsoMergeFD.p=IsoMergeFD.p/Num
73 IsoMergeTP.p=IsoMergeTP.p/Num
74 IsoMergeFN.p=IsoMergeFN.p/Num
75 IsoMergeTN.p=IsoMergeTN.p/Num
76 IsoMergeFDR=IsoMergeFDR/Num
77 IsoMergeTPR=IsoMergeTPR/Num
78 IsoMergeFPR=IsoMergeFPR/Num
80 PlotTopName=paste(paste(Path,paste("Top","Iso","DVD",IsoMergeDVD[1], IsoMergeDVD[2],"Sample",NumSample, sep="_"),sep=""),".pdf",sep="")
82 TrueDELength=length(unlist(IsoSIMout[[i]]$TrueDE)[unlist(IsoSIMout[[i]]$TrueDE)%in%EBSeqNames])
84 PlotTopCts(TrueDELength,IsoMergeFD[1:TrueDELength,],c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
88 PlotFDName=paste(paste(Path,paste("FDTP","Iso","DVD",IsoMergeDVD[1], IsoMergeDVD[2],"Sample",NumSample,sep="_"),sep=""),".pdf",sep="")
90 PlotFDTP(MinNumIso,IsoMergeFDR, IsoMergeTPR, c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
93 PlotFPName=paste(paste(Path,paste("FPRTP","Iso","DVD",IsoMergeDVD[1], IsoMergeDVD[2],"Sample",NumSample,sep="_"),sep=""),".pdf",sep="")
95 PlotFPTP(MinNumIso,IsoMergeFPR, IsoMergeTPR, c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
99 out=list(IsoMergeTable=IsoMergeTable, IsoMergeDVD=IsoMergeDVD, IsoMergePhi=IsoMergePhi, IsoMergeFD=IsoMergeFD)