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

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

diff --git a/EBSeq/demo/EBSeq.R b/EBSeq/demo/EBSeq.R
deleted file mode 100644 (file)
index 4ffc4a4..0000000
--- a/EBSeq/demo/EBSeq.R
+++ /dev/null
@@ -1,110 +0,0 @@
-library(EBSeq)
-set.seed(13)
-
-# Section 3.1
-
-GeneGenerate=GeneSimu(DVDconstant=4, DVDqt1=NULL, DVDqt2=NULL,
-  Conditions=rep(c(1,2),each=5), NumofSample=10, NumofGene=10000,
-  DEGeneProp=.1, Phiconstant=NULL, Phi.qt1=.1, Phi.qt2=.9,
-  Meanconstant=NULL, OnlyData=T)
-GeneData=GeneGenerate$data
-GeneTrueDENames=GeneGenerate$TrueDE
-str(GeneData)
-str(GeneTrueDENames)
-
-Sizes=MedianNorm(GeneData)
-
-EBres=EBTest(Data=GeneData, 
-  Conditions=as.factor(rep(c(1,2),each=5)),sizeFactors=Sizes, maxround=5)
-
-PP=GetPP(EBres)
-str(PP)
-DEfound=names(PP)[which(PP>=.95)]
-str(DEfound)
-sum(DEfound%in%GeneTrueDENames)
-
-QQP(QList=EBres$QList1, AlphaResult=EBres[[1]][5,1], 
-  BetaResult=EBres[[2]][5,1], name="Gene Simulation", AList="F", GroupName=NULL)
-DenNHist(QList=EBres$QList1, Alpha=EBres[[1]][5,1], Beta=EBres[[2]][5,1], 
-  name="Gene Simulation", AList="F", GroupName=NULL)
-
-# Section 3.2
-
-IsoGenerate=IsoSimu(DVDconstant=NULL, DVDqt1=.97, DVDqt2=.98, 
-  Conditions=as.factor(rep(c(1,2),each=5)), NumofSample=10, 
-  NumofIso=c(1000,2000,3000), DEIsoProp=.1, Phiconstant=NULL, 
-  Phi.qt1=.25, Phi.qt2=.75, OnlyData=T )
-str(IsoGenerate)
-
-IsoMat=do.call(rbind,IsoGenerate$data)
-str(IsoMat)
-
-IsoSizes=MedianNorm(IsoMat)
-
-IsoNames=rownames(IsoMat)
-str(IsoNames)
-GeneNames=paste("Gene",c(1:3000),sep="_")
-IsosGeneNames=c(GeneNames[1:1000],rep(GeneNames[1001:2000],each=2),
-  rep(GeneNames[2001:3000],each=3))
-NgList=GetNg(IsoNames, IsosGeneNames)
-IsoNgTrun=NgList$IsoformNgTrun
-IsoNgTrun[c(1:3,1001:1003,3001:3003)]
-
-IsoEBres=EBTest(Data=IsoMat, NgVector=IsoNgTrun, 
-  Conditions=as.factor(rep(c(1,2),each=5)),sizeFactors=IsoSizes, maxround=5)
-IsoPP=GetPP(IsoEBres)
-str(IsoPP)
-IsoDE=IsoPP[which(IsoPP>=.95)]
-str(IsoDE)
-sum(names(IsoDE)%in%IsoGenerate$TrueDE)
-
-par(mfrow=c(2,2))
-PolyFitValue=vector("list",3)
-for(i in 1:3)
-  PolyFitValue[[i]]=PolyFitPlot(IsoEBres$C1Mean[[i]], 
-    IsoEBres$C1EstVar[[i]],5)
-
-PolyAll=PolyFitPlot(unlist(IsoEBres$C1Mean), unlist(IsoEBres$C1EstVar),5)
-lines(log10(IsoEBres$C1Mean[[1]][PolyFitValue[[1]]$sort]), 
-  PolyFitValue[[1]]$fit[PolyFitValue[[1]]$sort],col="yellow")
-lines(log10(IsoEBres$C1Mean[[2]][PolyFitValue[[2]]$sort]), 
-  PolyFitValue[[2]]$fit[PolyFitValue[[2]]$sort],col="pink")
-lines(log10(IsoEBres$C1Mean[[3]][PolyFitValue[[3]]$sort]), 
-  PolyFitValue[[3]]$fit[PolyFitValue[[3]]$sort],col="green")
-legend("topleft",c("All Isoforms","Ng = 1","Ng = 2","Ng = 3"),
-  col=c("red","yellow","pink","green"),lty=1,lwd=3,box.lwd=2)
-
-par(mfrow=c(2,2))
-QQP(QList=IsoEBres$QList1, AlphaResult=IsoEBres[[1]][5,],
- BetaResult=IsoEBres[[2]][5,], 
- name="Isoforms", AList="F", GroupName=paste("Ng = ",c(1:3),sep=""))
-
-DenNHist(QList=IsoEBres$QList1, Alpha=IsoEBres[[1]][5,], 
-  Beta=IsoEBres[[2]][5,], 
-  name="Isoforms", AList="F", GroupName=paste("Ng = ",c(1:3),sep=""))
-
-# Section 3.3
-
-Conditions=c("C1","C1","C2","C2","C3","C3")
-PosParti=GetPatterns(Conditions)
-PosParti
-
-Parti=PosParti[-3,]
-Parti
-
-MultiData=GeneMultiSimu(Conditions=Conditions,AllParti=Parti,
-          NumofSample=6,NumofGene=1000,DEGeneProp=c(.7,.1,.1,.1),
-          DVDqt1=.98,DVDqt2=.99,Phi.qt1=.25,Phi.qt2=.75)
-str(MultiData)
-
-MultiSize=MedianNorm(MultiData$data)
-MultiRes=EBMultiTest(MultiData$data,NgVector=NULL,Conditions=Conditions,
-           AllParti=Parti, sizeFactors=MultiSize, maxround=5)
-MultiPP=GetMultiPP(MultiRes)
-names(MultiPP)
-MultiPP$PP[1:10,]
-MultiPP$MAP[1:10]
-MultiPP$Patterns
-sum(MultiPP$MAP==MultiData$Patterns)
-
-# EOF
\ No newline at end of file