2 function(GeneSIMout, Num, Path="./"){
3 NumSample=ncol(GeneSIMout[[i]]$generateData)
6 for (i in 1:Num)NumGene[i]=nrow(GeneSIMout[[i]]$generateData)
8 MinNumGene=min(NumGene)
9 AproxNumDE=length(GeneSIMout[[1]]$TrueDE)
11 GeneMergeTable=matrix(rep(0,12),nrow=6)
12 for(i in 1:Num)GeneMergeTable=GeneMergeTable+GeneSIMout[[i]][[1]]
13 GeneMergeTable=GeneMergeTable/Num
14 GeneMergeTable=round(GeneMergeTable,2)
17 for(i in 1:Num)GeneMergeDVD=GeneMergeDVD+GeneSIMout[[i]][[3]]
18 GeneMergeDVD=round(GeneMergeDVD/Num,2)
20 GeneMergePhi=matrix(rep(0,2),nrow=2)
21 for(i in 1:Num)GeneMergePhi=GeneMergePhi+GeneSIMout[[i]][[4]]
22 GeneMergePhi=round(GeneMergePhi/Num,2)
24 TXTname=paste(paste(Path,paste("Gene","DVD",GeneMergeDVD[1], GeneMergeDVD[2],"Phi",GeneMergePhi[1], GeneMergePhi[2],"Sample",NumSample,sep="_"),sep=""),".txt",sep="")
25 write.table(GeneMergeTable, file=TXTname)
28 ####### Note everytime # DE genes and # total genes may different. (since NA issue)
29 GeneMergeFD=matrix(rep(0,5*MinNumGene),ncol=5)
30 GeneMergeFD.p=matrix(rep(0,5*MinNumGene),ncol=5)
31 GeneMergeTP.p=matrix(rep(0,5*MinNumGene),ncol=5)
32 GeneMergeFN.p=matrix(rep(0,5*MinNumGene),ncol=5)
33 GeneMergeTN.p=matrix(rep(0,5*MinNumGene),ncol=5)
35 GeneMergeFDR=matrix(rep(0,5*MinNumGene),ncol=5)
36 GeneMergeTPR=matrix(rep(0,5*MinNumGene),ncol=5)
37 GeneMergeFPR=matrix(rep(0,5*MinNumGene),ncol=5)
41 # Make sure names in the same order
42 # Get FD number for each number of genes found
43 TotalNum=nrow(GeneSIMout[[i]]$generateData)
44 NumDE=length(GeneSIMout[[i]]$TrueDE)
45 EBSeqNames=names(GeneSIMout[[i]]$EBSeqPP)
46 tmpMatrix=cbind(GeneSIMout[[i]]$DESeqP[EBSeqNames],GeneSIMout[[i]]$edgeRP[EBSeqNames], exp(GeneSIMout[[i]]$BaySeqPP[EBSeqNames,2]),GeneSIMout[[i]]$BBSeqP[EBSeqNames],GeneSIMout[[i]]$EBSeqPP)
47 # Bayseq and EBseq are PP. Others are p value
48 tmpFD=TopCts(tmpMatrix, c(0,0,1,0,1), GeneSIMout[[i]]$TrueDE[GeneSIMout[[i]]$TrueDE%in%EBSeqNames], MinNumGene)
49 # Get percentage for FP, TP, TN, FN!
50 tmpFD.p=tmpFD/TotalNum
52 tmpTP.p=(c(1:MinNumGene)-tmpFD)/TotalNum
54 tmpFN.p=NumDE/TotalNum - tmpTP.p
56 tmpTN.p=(TotalNum-NumDE)/TotalNum - tmpFD.p
59 tmpFDR=tmpFD.p/(tmpFD.p+tmpTP.p)
60 tmpFPR=tmpFD.p/(tmpFD.p+tmpTN.p)
61 tmpTPR=tmpTP.p/(tmpFN.p+tmpTP.p)
62 GeneMergeFDR=GeneMergeFDR+tmpFDR
63 GeneMergeTPR=GeneMergeTPR+tmpTPR
64 GeneMergeFPR=GeneMergeFPR+tmpFPR
66 GeneMergeFD.p=GeneMergeFD.p+tmpFD.p
67 GeneMergeTP.p=GeneMergeTP.p+tmpTP.p
68 GeneMergeFN.p=GeneMergeFN.p+tmpFN.p
69 GeneMergeTN.p=GeneMergeTN.p+tmpTN.p
71 GeneMergeFD=GeneMergeFD+tmpFD
73 GeneMergeFD=GeneMergeFD/Num
74 GeneMergeFD.p=GeneMergeFD.p/Num
75 GeneMergeTP.p=GeneMergeTP.p/Num
76 GeneMergeFN.p=GeneMergeFN.p/Num
77 GeneMergeTN.p=GeneMergeTN.p/Num
79 GeneMergeFDR=GeneMergeFDR/Num
80 GeneMergeTPR=GeneMergeTPR/Num
81 GeneMergeFPR=GeneMergeFPR/Num
84 PlotTopName=paste(paste(Path,paste("Top","Gene","DVD",GeneMergeDVD[1], GeneMergeDVD[2],"Phi",GeneMergePhi[1], GeneMergePhi[2],"Sample",NumSample, sep="_"),sep=""),".pdf",sep="")
86 TrueDELength=length(GeneSIMout[[i]]$TrueDE[GeneSIMout[[i]]$TrueDE%in%EBSeqNames])
88 PlotTopCts(TrueDELength,GeneMergeFD[1:TrueDELength,],c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
92 PlotFDName=paste(paste(Path,paste("FDTP","Gene","DVD",GeneMergeDVD[1], GeneMergeDVD[2],"Phi",GeneMergePhi[1], GeneMergePhi[2],"Sample",NumSample,sep="_"),sep=""),".pdf",sep="")
94 PlotFDTP(MinNumGene,GeneMergeFDR, GeneMergeTPR, c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
97 PlotFPName=paste(paste(Path,paste("FPRTP","Gene","DVD",GeneMergeDVD[1], GeneMergeDVD[2],"Phi",GeneMergePhi[1], GeneMergePhi[2],"Sample",NumSample,sep="_"),sep=""),".pdf",sep="")
99 PlotFPTP(MinNumGene,GeneMergeFPR, GeneMergeTPR, c("DESeq","edgeR","BaySeq","BBSeq","EBSeq"))
103 out=list(GeneMergeTable=GeneMergeTable, GeneMergeDVD=GeneMergeDVD, GeneMergePhi=GeneMergePhi, GeneMergeFD=GeneMergeFD)