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CONY.R
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WindowInfo=function(target.df, RefFaFileName="chr20.fa", WindowSize=100){
library(exomeCopy)
library(IRanges)
colnames(target.df)=c("seqnames","start","end")
RefFaFile =scanFa(RefFaFileName)
CalIRange=function(start,end,WindowSize){
NofW= ceiling((end-start+1)/ WindowSize)
Istart= start+(c(1:(NofW))-1)* WindowSize
IRangesSep = IRanges(Istart, width= WindowSize)
end(IRangesSep[length(IRangesSep)])= end
return(c(IRangesSep= IRangesSep, NofW = NofW))
}
IRangesSepF=CalIRange(target.df$start[1], target.df$end[1],WindowSize)
IRangesSep=IRangesSepF$IRangesSep
IRNumber= IRangesSepF$ NofW
if(nrow(target.df)>1){
for(i in 2:nrow(target.df)){
IRangesSepF=CalIRange(target.df$start[i],target.df$end[i],WindowSize)
IRangesSepT=IRangesSepF $ IRangesSep
IRangesSep =c(IRangesSep, IRangesSepT)
IRNumberT=IRangesSepF $ NofW
IRNumber=c(IRNumber, IRNumberT)
}}
target <- GRanges(seqname= rep(target.df$seqname, IRNumber), ranges=IRangesSep)
rdata <- RangedData(space=seqnames(target),ranges=ranges(target))
IRangeSE=cbind(start(rdata), end(rdata))
colnames(IRangeSE)=c("start","end")
IRangeSE=as.data.frame(IRangeSE)
nonAmb=function(IRangeSE, start,end, RefFaFile){
return(letterFrequency (narrow(RefFaFile, start= IRangeSE[start], end= IRangeSE [end]), "ATCG", as.prob=T))
}
#rdata[[nonAmb]] =apply(IRangeSE, MARGIN=1, nonAmb, start= "start", end="end", RefFaFile = RefFaFile)
nonAmb=apply(IRangeSE, MARGIN=1, nonAmb, start= "start", end="end", RefFaFile = RefFaFile)
GCcontent=function(IRangeSE ,start, end, Fa){
return(letterFrequency (narrow(RefFaFile, start= IRangeSE[start], end= IRangeSE [end]), "GC", as.prob=T))
}
GC= apply(IRangeSE, MARGIN=1, GCcontent, start= "start", end="end", Fa= RefFaFile)
CONY.TempRegion=cbind(rep(noquote(names(rdata)),nrow(rdata)),start(rdata), end(rdata),width(rdata), nonAmb,GC)
return(CONY.TempRegion)
write.table(CONY.TempRegion, "CONY.TempRegion.txt",quote = F, sep = " ",row.names = F,col.names =c("seq","start","end","width","nonAmb","GC"))
}
################################################################################################################################################################################################################
CalRD=function(TempRegion, CRDMethod=c("PointR","SumUp"), SampleBamFileName= "aln1101.final.sorted.bam", MPileCountFileName="aln1101.Used.txt",SampleName="Sample1101",TargetChr="chr20", WindowSize=100){
library(exomeCopy)
library(IRanges)
if(CRDMethod=="PointR"){
IRangesSep =IRanges(start=TempRegion$start, end=TempRegion$end)
target <- GRanges(seqname= rep(TargetChr, nrow(TempRegion)), ranges=IRangesSep)
rdata <- RangedData(space=seqnames(target),ranges=ranges(target))
scanBamHeader(SampleBamFileName)[[1]]$targets
levels(seqnames(target))
ARD=countBamInGRanges(SampleBamFileName,target)
write.table(cbind(TempRegion,ARD), paste("CONY.1-TempRegion.",TargetChr,".",SampleName,".PointR.RD.txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
return(cbind(TempRegion,ARD))
}
if(CRDMethod=="SumUp"){
MPileCount=read.table(MPileCountFileName, header=F)
colnames(MPileCount)=c("location","count")
MPileCount=as.data.frame(MPileCount)
RDVec=rep(0,TempRegion$end[nrow(TempRegion)])
RDVec[MPileCount[,1]]= MPileCount[,2]
RDVec=c(RDVec, rep(0,(100-length(RDVec)%%100)) )
RDMatrix=matrix(RDVec,100,ceiling(length(RDVec)/100))
SRD=colSums(RDMatrix)
#ARD= SRD* WindowSize /(TempRegion$nonAmb * TempRegion$width)
ARD= SRD /(TempRegion$nonAmb * TempRegion$width)
write.table(cbind(TempRegion,ARD), paste("CONY.1-TempRegion.",TargetChr,".",SampleName,".SumUp.RD.txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
return(cbind(TempRegion,ARD))
}
}
##################################################################################################################################################################################################################
AdjRD=function(CRDMethod=c("PointR","SumUp"), TargetChr, SampleName){
if(CRDMethod=="PointR"){
TempRegion=read.table(paste("CONY.1-TempRegion.",TargetChr,".",SampleName,".PointR.RD.txt", sep=""),header=T)
}
if(CRDMethod=="SumUp"){
TempRegion=read.table(paste("CONY.1-TempRegion.",TargetChr,".",SampleName,".SumUp.RD.txt", sep=""), header=T)
}
TempInx=which( (TempRegion$GC>=0.2) & (TempRegion$GC<=0.8) & (TempRegion$ARD!="NaN") &(TempRegion$ARD!=0))
LOWS=lowess(TempRegion$ARD [TempInx]~TempRegion$GC[TempInx])
MLS=mean(LOWS$y)
AdjRD= TempRegion$ARD
T.GC=c(20:80)/100
T.RD=rep(0,length(T.GC))
for( i in 1:length(T.GC)){
T.RD[i]= LOWS$y[which(LOWS$x== T.GC [i])] [1]
}
AdjRD[TempInx]= TempRegion$ARD[TempInx]* MLS /T.RD[ match(round(TempRegion$GC[TempInx],2) ,T.GC)]
TempRegion=cbind(TempRegion, AdjRD)
write.table(TempRegion, paste("CONY.2-TempRegion.",TargetChr,".",SampleName, ".", CRDMethod ,".AdjRD.txt", sep="") ,quote = F, sep = " ",row.names = F,col.names =T)
}
####################################################################################################################################################################################################################
UsedRD=function(CRDMethod=c("PointR","SumUp"), AnaMethod=c("Single","Paired"), TargetChr, SampleName,ControlName){
if(AnaMethod=="Single"){
TempRegion= read.table(paste("CONY.2-TempRegion.",TargetChr,".",SampleName, ".", CRDMethod , ".AdjRD.txt", sep=""),header=T)
NonInf=which((is.na(TempRegion$AdjRD)==T)| (TempRegion$nonAmb<0.5))
NonInfRegion=TempRegion[NonInf,]
write.table(NonInfRegion, paste("CONY.3-NonInfRegion.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod, ".txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
TempRegion= TempRegion[-NonInf,]
CN0=which(TempRegion$AdjRD==0)
CN0Region=TempRegion[CN0,]
write.table(CN0Region, paste("CONY.3-CN0Region.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod,".txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
TempRegion= TempRegion[-CN0,]
RD=TempRegion$AdjRD
target=rep(1,length(RD))
write.table(cbind(TempRegion,RD, target), paste("CONY.3-TempRegion.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod ,".UsedRD.txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
}
if(AnaMethod=="Paired"){
TempRegion1= read.table(paste("CONY.2-TempRegion.",TargetChr,".",SampleName, ".", CRDMethod ,".AdjRD.txt", sep=""),header=T)
TempRegion2= read.table(paste("CONY.2-TempRegion.",TargetChr,".",ControlName, ".", CRDMethod ,".AdjRD.txt", sep=""),header=T)
NonInf=which((is.na(TempRegion1$AdjRD)==T)| (TempRegion1$nonAmb<0.5))
NonInfRegion=TempRegion1[NonInf,]
write.table(NonInfRegion, paste("CONY.3-NonInfRegion.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod, ".txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
TempRegion1= TempRegion1[-NonInf,]
TempRegion2= TempRegion2[-NonInf,]
Both0=which((TempRegion1$AdjRD==0)& (TempRegion2$AdjRD==0))
CN0=which((TempRegion1$AdjRD==0)& (TempRegion2$AdjRD!=0))
CNG=which((TempRegion1$AdjRD!=0)& (TempRegion2$AdjRD==0))
Both0Region= TempRegion1[Both0,]
CN0Region= TempRegion1[CN0,]
CNGRegion= TempRegion1[CNG,]
write.table(Both0Region, paste("CONY.3-Both0Region.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod,".txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
write.table(CN0Region, paste("CONY.3-CN0Region.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod,".txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
write.table(CNGRegion, paste("CONY.3-CNGRegion.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod,".txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
Del=sort(c(Both0, CN0, CNG))
TempRegion1= TempRegion1[-Del,]
TempRegion2= TempRegion2[-Del,]
RD=TempRegion1$AdjRD/ TempRegion2$AdjRD
target=rep(1,length(RD))
TempRegion=cbind(TempRegion1,RD,target)
write.table(TempRegion, paste("CONY.3-TempRegion.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod ,".UsedRD.txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
}
}
#######################################################################################################################################################################################################################
EstPar=
function(CRDMethod=c("PointR","SumUp"), AnaMethod=c("Single","Paired"), TargetChr, SampleName, NCN) {
TempRegion=read.table(paste("CONY.3-TempRegion.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod ,".UsedRD.txt", sep=""),header=T)
# mean of CN2
Med0=median(na.omit(log(TempRegion$RD)))
# var of CN2
logV=((sort(log(TempRegion$RD),decreasing = T)[round(nrow(TempRegion) *.025)]- Med0)/1.96)^2
#estimate the mean and variance for each CN state
Mean2=exp(Med0+logV/2)
Var2=(exp(logV) -1)*exp(2*Med0+logV)
OMean=Mean2*(c(1: NCN)/2)
OVar= Var2*(c(1: NCN)/2)
GroupMean =log(OMean^2/((OVar+OMean^2)^0.5))
GroupVar =log(1+(OVar/((OMean)^2)))
#estimate of proportion of each CN state
AllP=matrix(rep(0,NCN),NCN,length(TempRegion$RD),byrow=T)
for(i in 1:NCN){
AllP[i,]= dlnorm((TempRegion$RD),GroupMean[i],(GroupVar[i])^0.5)
}
AsP=as.numeric(apply(t(abs(AllP)), 1, which.max))
GroupPro=rep(0,NCN)
for(i in 1:NCN){
GroupPro[i]=length(which(AsP==i))/length(TempRegion$RD)
}
GroupCNV=c(1:NCN)
(NCN);(GroupMean);(GroupVar);(GroupPro);(GroupCNV)
GroupSumm=cbind(GroupCNV,GroupMean,GroupVar,GroupPro)
colnames(GroupSumm)=c("GroupCNV","GroupMean","GroupVar","GroupPro")
write.table(GroupSumm, paste("CONY.3-GroupSumm.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod ,".txt", sep=""),quote = F, sep = " ",row.names =F,col.names =T)
}
#######################################################################################################################################################################################################################
RunCONY= function(CRDMethod=c("PointR","SumUp"), AnaMethod=c("Single","Paired"), TargetChr, SampleName, RunTime = 300000,BurnN = 5000,RTN = 1000,BCPoint = 20, FragLength=500000){
TempRegion=read.table(paste("CONY.3-TempRegion.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod ,".UsedRD.txt", sep=""),header=T)
GroupSumm=read.table(paste("CONY.3-GroupSumm.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod ,".txt", sep=""),header =T)
RunCONYParallel=function(Frag,AFrag,TempRegion, GroupSumm, RunTime = 300000,BurnN = 5000,RTN = 1000,BCPoint = 20, TargetChr, SampleName) {
TempRegion= TempRegion[(ceiling((Frag-1)*nrow(TempRegion)/AFrag)+1): (ceiling(Frag*nrow(TempRegion)/AFrag)),]
SetIni=function(TempRegion,GroupSumm){
### Setting fixed parameters
print("setting fixed parameters")
RD=log(TempRegion$RD)
if(length(which(RD==Inf))>0){RD[(which(RD==Inf))]=NA }
if(length(which(RD==(-Inf)))>0){RD[(which(RD==(-Inf)))]=NA }
Inx_AD=TempRegion$start
RDsq=RD^2
target=TempRegion$target
MeanF= GroupSumm$GroupMean
GroupN= nrow(GroupSumm)
AlphaF=rep(5, GroupN)
GroupPro= GroupSumm$ GroupPro
GroupVar= GroupSumm$GroupVar
GroupCNV= GroupSumm$ GroupCNV
KappaF=GroupPro*length(RD)
KappaF[which(GroupPro==0)]=1
BetaF=((AlphaF-1)*GroupVar*KappaF)/( KappaF+1)
LambdaF=0.5
WeightIni=GroupPro
WeightUp=matrix(0,length(GroupPro),length(GroupPro))
for(i in 1: length(GroupPro)){
WeightUp[i,]=GroupPro
for(j in 1: length(GroupPro)){
WeightUp[i,j]=GroupPro[j]/(1-GroupPro[i])
}
WeightUp[i,i]=0
}
GroupPartLog=rep(0, GroupN)
for(k in 1:GroupN){
GroupPartLog[k]=log((BetaF[k]^AlphaF[k])* (KappaF[k]^0.5) / gamma(AlphaF[k]))
}
#### Breakpoint initial
### setting breakpoint gap breakpoint & last one
print("setting initial")
if(TempRegion$target[nrow(TempRegion)]==0){
BrFix=sort(c(which(TempRegion$target==0), (which(TempRegion$target==0))-1) )
if(TempRegion$target[1]==0){
BrFix= BrFix[-1]
}
}
if(TempRegion$target[nrow(TempRegion)]!=0){
BrFix=sort(c(which(TempRegion$target==0), (which(TempRegion$target==0))-1) )
if(TempRegion$target[1]==0){
BrFix= BrFix[-1]
}
BrFix=c(BrFix, nrow(TempRegion))
}
if(length(BrFix)==1){CNRUpBr=matrix(c(0,BrFix),1,2)}
if(length(BrFix)>1){
if(TempRegion$target[1]==0){
CNRUpBr=matrix(0, floor(length(BrFix) /2),2)
for(i in 1: (floor(length(BrFix) /2))){
CNRUpBr[i,]=c(BrFix[2*i-1],BrFix[2*i])
}
}
if(TempRegion$target[1]==1){
CNRUpBr=matrix(0, floor(length(BrFix) /2)+1,2)
CNRUpBr[1,]=c(0,BrFix[1])
for(i in 2: (floor(length(BrFix) /2)+1)){
CNRUpBr[i,]=c(BrFix[2*i-2],BrFix[2*i-1])
}
}
}
#### breakpoint
SRM=smooth.spline(na.omit(RD))
SRD=rep(NA,length(RD))
SRMX =which(is.na(RD)==F)
SRD[SRMX]= SRM$y
SRDT=SRM$y
SRD1=SRDT[1: (length(SRDT)-1)]
SRD2=SRDT[2: (length(SRDT))]
LowB=0.02
UppB=0.98
BrInxT=sort(which( ((SRD1<quantile(SRDT,LowB))&(SRD2>=quantile(SRDT,LowB)))
|
((SRD1>quantile(SRDT,LowB))&(SRD2<=quantile(SRDT,LowB)))
|
((SRD1<quantile(SRDT,UppB))&(SRD2>=quantile(SRDT,UppB)))
|
((SRD1>quantile(SRDT,UppB))&(SRD2<=quantile(SRDT,UppB)))
))
BrInxO= SRMX [BrInxT]
if(length(which(is.na(match(BrInxO,BrFix))==F))!=0){
BrInxO= BrInxO[-(which(is.na(match(BrInxO,BrFix))==F))]
}
BrInx=sort(c(BrInxO,BrFix))
if(is.na(match(length(RD),BrInx))==T){ BrInx =c(BrInx,length(RD))}
Br=rep(0,length(RD))
Br[BrInx]=1
## CN initial
CNVTargetInx=rep(0,length(BrInx))
if(BrFix[1]==1){
for(i in 2:length(BrInx)){
CNVTargetInx[i]=TempRegion$target[BrInx[i]]
}
}
if(BrFix[1]!=1){
for(i in 1:length(BrInx)){
CNVTargetInx[i]=TempRegion$target[BrInx[i]]
}}
CNR=rep(0,length(BrInx))
CNR[which(CNVTargetInx==1)]= rep(c(1:GroupN), ceiling (length(which(CNVTargetInx==1))/GroupN)) [1: (length(which(CNVTargetInx==1)))]
return(list("TempRegion"=TempRegion,"BrFix"=BrFix, "BrInx"=BrInx, "Br"= Br , "CNRUpBr"= CNRUpBr , "CNR"=CNR ,"RD"=RD ,"RDsq"=RDsq ,"GroupN"=GroupN ,"MeanF"=MeanF ,"AlphaF"=AlphaF ,"KappaF"=KappaF ,"BetaF"=BetaF ,"LambdaF"=LambdaF ,"WeightIni"=WeightIni, "WeightUp"=WeightUp, "GroupPartLog"= GroupPartLog, "GroupCNV"= GroupCNV))
}
DP3=SetIni(TempRegion,GroupSumm)
TempRegion=DP3$TempRegion
RD=DP3$RD
RDsq=DP3$ RDsq
GroupN=DP3$ GroupN
MeanF=DP3$ MeanF
BetaF=DP3$ BetaF
AlphaF=DP3$ AlphaF
KappaF=DP3$ KappaF
LambdaF=DP3$ LambdaF
WeightIni=DP3$ WeightIni
WeightUp=DP3$ WeightUp
GroupPartLog=DP3$ GroupPartLog
CNR=DP3$ CNR
BrInx=DP3$ BrInx
GroupCNV=DP3$ GroupCNV
BrFix=DP3$ BrFix
CNRUpBr=DP3$ CNRUpBr
target=TempRegion$target
#source("DataPrep5N.r")
source("CONY.R")
tic<- Sys.time()
CNRUp=UpC(RD,RDsq,GroupN,MeanF,BetaF,AlphaF,KappaF,LambdaF,WeightIni,WeightUp ,GroupPartLog,CNR,BrInx,GroupCNV,BrFix,CNRUpBr)
toc<- Sys.time()
comp.time<- toc - tic
print(comp.time)
CNMode=matrix(0,GroupN,length(RD))
BFInxTemp=rep(0,length(RD))
BFDiff=matrix(NA,1,2)
colnames(BFDiff)=c("times","diff")
tor=0/length(RD)
for(i in 2:BurnN){
tp=sample(c(1,2,3,4),1,prob=c( ( (GroupN-1)/(GroupN*3)),(1/3),(1/(GroupN*3)), (1/3) ) )
print(c(i,tp))
BB=switch(tp,Spt(RD, RDsq, GroupN,MeanF, BetaF,AlphaF,KappaF,LambdaF, WeightIni,WeightUp, GroupPartLog,CNRUp,BrInx,GroupCNV,BrFix,CNRUpBr), Meg(RD, RDsq, GroupN,MeanF, BetaF,AlphaF,KappaF,LambdaF, WeightIni,WeightUp, GroupPartLog,CNRUp,BrInx,GroupCNV,BrFix,CNRUpBr),DBSpt(RD, RDsq, GroupN,MeanF, BetaF,AlphaF,KappaF,LambdaF, WeightIni,WeightUp, GroupPartLog,CNRUp,BrInx,GroupCNV,BrFix,CNRUpBr),Cbound(RD, RDsq, GroupN,MeanF, BetaF,AlphaF,KappaF,LambdaF, WeightIni,WeightUp, GroupPartLog,CNRUp,BrInx,GroupCNV,BrFix,CNRUpBr) )
CNRUp=BB$CNRUpN
BrInx=BB$BrInxN
#ChangInx=BB$ChangInx
print(c (BB$Type,BB$Result))
print(c("Number of Breakpoint",length(BB$BrInxN)))
if(BB$Result=="Success" ){
tic<- Sys.time()
CNRUp= UpC (RD,RDsq,GroupN,MeanF,BetaF,AlphaF,KappaF,LambdaF,WeightIni,WeightUp ,GroupPartLog,CNR= BB$CNRUpN,BrInx= BB$BrInxN,GroupCNV,BrFix,CNRUpBr)
toc<- Sys.time()
comp.time<- toc - tic
print(comp.time)
}
gc()
}
SuccessPro=0
SuccessProVec=0
for(i in (BurnN+1):RunTime){
tp=sample(c(1,2,3,4),1,prob=c(( (GroupN-1)/(GroupN*3)),(1/3),(1/(GroupN*3)), (1/3)))
print(c(i,tp))
BB=switch(tp,Spt(RD, RDsq, GroupN,MeanF, BetaF,AlphaF,KappaF,LambdaF, WeightIni,WeightUp, GroupPartLog,CNRUp,BrInx,GroupCNV,BrFix,CNRUpBr), Meg(RD, RDsq, GroupN,MeanF, BetaF,AlphaF,KappaF,LambdaF, WeightIni,WeightUp, GroupPartLog,CNRUp,BrInx,GroupCNV,BrFix,CNRUpBr),DBSpt(RD, RDsq, GroupN,MeanF, BetaF,AlphaF,KappaF,LambdaF, WeightIni,WeightUp, GroupPartLog,CNRUp,BrInx,GroupCNV,BrFix,CNRUpBr),Cbound(RD, RDsq, GroupN,MeanF, BetaF,AlphaF,KappaF,LambdaF, WeightIni,WeightUp, GroupPartLog,CNRUp,BrInx,GroupCNV,BrFix,CNRUpBr) )
CNRUp=BB$CNRUpN
BrInx=BB$BrInxN
if(BB$Result=="Success"){
SuccessPro=SuccessPro+1
CNRUp= UpC (RD,RDsq,GroupN,MeanF,BetaF,AlphaF,KappaF,LambdaF,WeightIni,WeightUp ,GroupPartLog,CNR= BB$CNRUpN,BrInx= BB$BrInxN,GroupCNV,BrFix,CNRUpBr)
}
CNModeTemp= CNRWin (RD,CNRUp,BrInx)
CNModeTS=matrix(0,GroupN,length(CNModeTemp))
for(j in 1:GroupN){
CNModeTS[j,which(CNModeTemp==j)]=1
}
CNMode= CNMode+ CNModeTS
rm(CNModeTS)
if( (i%%RTN)==0){
BFDec=matrix(0,GroupN,length(RD))
BFInx=rep(0,length(RD))
SuccessProVec=c(SuccessProVec,SuccessPro/(i-BurnN))
for(m in 1:GroupN){
BFDec[m,]=(CNMode[m,]/CNMode[2,])/( WeightIni[m]/ WeightIni[2])
}
for(j in 1:length(RD)){
if(target[j]==0){BFInx[j]=0}
if(target[j]!=0) {
if( max(na.omit(BFDec[,j])) >BCPoint ){ BFInx[j]=which.max(BFDec[,j]) }
if( max(na.omit(BFDec[,j])) <=BCPoint ){ BFInx[j]=2 }
}
}
rm(BFDec)
BFDiffT= length(which(BFInx!=BFInxTemp))/length(RD)
BFDiffTM=matrix(c(i, BFDiffT),1,2)
BFDiff=rbind(BFDiff,BFDiffTM)
BFInxTemp=BFInx
print(BFDiff)
gc()
if(BFDiffT<=tor){break}
}
gc()
}
return(BFInxTemp)
}
source("http://bioconductor.org/biocLite.R")
biocLite("snow")
library(snow)
AFrag=floor(sum(TempRegion$width)/FragLength)
cl <- makeCluster(AFrag)
AA=matrix(c(1:AFrag), AFrag, 1)
source("CONY.R")
CN =parRapply(cl, AA, RunCONYParallel, AFrag,TempRegion, GroupSumm, RunTime,BurnN,RTN,BCPoint, TargetChr, SampleName)
stopCluster(cl)
write.table(cbind(TempRegion,CN),paste("CONY.4-Result.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod,".txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
}
#######################################################################################################################################################################################################################
ComResult=function(CRDMethod="PointR", AnaMethod="Single", TargetChr="chr20", SampleName="Sample1101"){
CONYResultT=read.table(paste("CONY.4-Result.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod,".txt", sep=""),header=T)
TempRegionFull=read.table(paste("CONY.2-TempRegion.",TargetChr,".",SampleName,".", CRDMethod ,".AdjRD.txt", sep=""),header=T)
CN=rep(NA,nrow(TempRegionFull))
TempRegionFull=cbind(TempRegionFull,CN)
ResultInx=match(CONYResultT$start, TempRegionFull$start)
TempRegionFull$CN[ResultInx]= CONYResultT$CN
if(AnaMethod=="Single"){
CN0Region=read.table(paste("CONY.3-CN0Region.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod,".txt", sep=""),header=T)
CN0Inx= match(CN0Region$start, TempRegionFull$start)
TempRegionFull$CN[CN0Inx]= 0
}
if(AnaMethod=="Paired"){
Both0Region= read.table(paste("CONY.3-Both0Region.",TargetChr,".",SampleName, ".", CRDMethod , ".", AnaMethod,".txt", sep=""),header=T)
CN0Region= read.table(paste("CONY.3-CN0Region.",TargetChr,".",SampleName[1], ".", CRDMethod , ".", AnaMethod,".txt", sep=""),header=T)
CNGRegion= read.table(paste("CONY.3-CNGRegion.",TargetChr,".",SampleName[1], ".", CRDMethod , ".", AnaMethod,".txt", sep=""),header=T)
Both0Inx= match(Both0Region$start, TempRegionFull$start)
CN0Inx= match(CN0Region$start, TempRegionFull$start)
CNGInx= match(CNGRegion$start, TempRegionFull$start)
TempRegionFull$CN[Both0Inx]=2
TempRegionFull$CN[CN0Inx]=0
TempRegionFull$CN[CNGInx]=9
}
write.table(TempRegionFull, paste("CONY.Result.",TargetChr,".",SampleName,".", CRDMethod, ".", AnaMethod ,".Window.txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
TempRegionFullCNTemp=TempRegionFull$CN
TempRegionFullCNTemp [which(is.na(TempRegionFullCNTemp)==T)]=-1
TempRegionFullCN1= TempRegionFullCNTemp [-1]
TempRegionFullCN2= TempRegionFullCNTemp [-nrow(TempRegionFull)]
TempRegionFullCND=TempRegionFullCN1- TempRegionFullCN2
Breakpoint=c(0,which(TempRegionFullCND!=0), nrow(TempRegionFull))
CONY.CNVResult=matrix(,length(Breakpoint)-1,3)
colnames(CONY.CNVResult)=c("start","end","CN")
CONY.CNVResult=as.data.frame(CONY.CNVResult)
for(i in 1: (length(Breakpoint)-1)){
CONY.CNVResult$start[i]= TempRegionFull$start[(Breakpoint[i]+1) ]
CONY.CNVResult$end[i]= TempRegionFull$end[Breakpoint[(i+1)]]
CONY.CNVResult$CN[i]= TempRegionFull$CN[(Breakpoint[i]+1)]
}
CONY.CNV= CONY.CNVResult [which((is.na(CONY.CNVResult$CN)==F)& (CONY.CNVResult$CN!=2)),]
write.table(CONY.CNVResult, paste("CONY.Result.",TargetChr,".",SampleName,".", CRDMethod, ".", AnaMethod ,".CNRegionAll.txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
write.table(CONY.CNV, paste("CONY.Result.",TargetChr,".",SampleName,".", CRDMethod, ".", AnaMethod ,".CNV.txt", sep=""),quote = F, sep = " ",row.names = F,col.names =T)
}
########################################################################################################################################################################################################################
### Update C step by step 1010 2013 delete front and back
UpC<-function(RD,RDsq,GroupN,MeanF,BetaF,AlphaF,KappaF,LambdaF,WeightIni,WeightUp ,GroupPartLog,CNR,BrInx,GroupCNV,BrFix,CNRUpBr){
BrInxT=c(0,BrInx)
for(i in 1:length(BrInx)){
if(CNR[i]!=0){
CNVComb=matrix(CNR,GroupN,length(CNR),byrow=T)
TS=rep(0,GroupN)
for(j in 1:GroupN){
CNVComb[j,i]=GroupCNV[j]
GS=sum(GroupPartLog[CNVComb[j,]])
WS=WeightPartL (WeightIni,WeightUp, CNR= CNVComb[j,],GroupN,CountMatrix= CountC (CNR= CNVComb[j,],GroupN))
RS=RegionPartL (RD,RDsq, Wstart= BrInxT[i]+1 ,Wend= BrInxT[i+1],CNR= CNVComb[j,i],MeanF,BetaF,AlphaF,KappaF)
TS[j]=GS+WS+RS
#print(c(GS,WS,RS,TS))
}
inx=order(TS,decreasing=T)
if( (i!=1) & (i!= length(BrInx))){
print("1")
if((CNR[i-1]!=0) & ( CNR[i+1]!=0)){
print("1.1")
CND=c(CNR[i-1], CNR[i+1])
CNR=CNVComb [inx[which(is.na(match(inx,CND)!=T))[1]],]
}
if((CNR[i-1]!=0) & ( CNR[i+1]==0)){
print("1.2")
CND=CNR[i-1]
CNR=CNVComb [inx[which(is.na(match(inx,CND)!=T))[1]],]
}
if((CNR[i-1]==0) & ( CNR[i+1]!=0)){
print("1.3")
CND=CNR[i+1]
CNR=CNVComb [inx[which(is.na(match(inx,CND)!=T))[1]],]
}
if((CNR[i-1]==0) & ( CNR[i+1]==0)){
print("1.4")
CNR=CNVComb [inx[1],]
}
}
if( (i==1) & (i!= length(BrInx))){
print("2")
if(CNR[i+1]!=0){
print("2.1")
CND=CNR[i+1]
CNR=CNVComb [inx[which(is.na(match(inx,CND)!=T))[1]],]
}
if( CNR[i+1]==0){
print("2.2")
CNR=CNVComb [inx[1],]
}
}
if( (i!=1) & (i== length(BrInx))){
print("3")
if(CNR[i-1]!=0){
print("3.1")
CND=CNR[i-1]
CNR=CNVComb [inx[which(is.na(match(inx,CND)!=T))[1]],]
}
if( CNR[i-1]==0){
print("3.2")
CNR=CNVComb [inx[1],]
}
}
if( (i==1) & (i== length(BrInx))){
print("4")
CNR=CNVComb [inx[1],]
}
}
if(CNR[i]==0){CNR=CNR}
}
return(CNR)
}
### Step 4.1 Merge
Meg<-function(RD, RDsq, GroupN,MeanF, BetaF,AlphaF,KappaF,LambdaF, WeightIni,WeightUp, GroupPartLog,CNRUp,BrInx,GroupCNV,BrFix,CNRUpBr){
BrInxO=sort(BrInx[-(match(BrFix,BrInx))])
DecPro=0
if(length(BrInxO)==0){DecPro =0}
if(length(BrInxO)!=0){
if(length(BrInxO)==1){CPoint=BrInxO}
if(length(BrInxO)>1){CPoint=sample(BrInxO,1)}
ChangInx=which((CNRUpBr[,1]<CPoint) &(CNRUpBr[,2]>CPoint))
#CN Region
UPCNInx=which(BrInx==CPoint)
CNRTC=sample(c(1,2),1)
CNRT=switch(CNRTC, CNRUp[UPCNInx], CNRUp[UPCNInx+1])
#General Form
if( ( (UPCNInx==1)& (is.na(match(CNRT,CNRUp[UPCNInx+2]))==T) ) | ( (UPCNInx>1)& (is.na(match(CNRT,c(CNRUp[UPCNInx-1],CNRUp[UPCNInx+2])))==T) ) ){
print("GeneralFormMerge")
CNRUpN=CNRUp;CNRUpN[UPCNInx]=CNRT;CNRUpN=CNRUpN[-(UPCNInx+1)]
BrInxN=BrInx[-(UPCNInx)]
WSN=WeightPartL(WeightIni,WeightUp, CNRUpN,GroupN, CountMatrix= as.matrix(CountC(CNRUpN,GroupN)))
WSO=WeightPartL(WeightIni,WeightUp, CNRUp,GroupN, CountMatrix= as.matrix(CountC(CNRUp,GroupN)))
GSN= GroupPartLog[CNRT]
GSO=sum(GroupPartLog[c(CNRUp[UPCNInx], CNRUp[UPCNInx+1])])
if(UPCNInx==1){WstartN=1;WstartO1=1}
if(UPCNInx>1){WstartN=BrInx[UPCNInx-1]+1; WstartO1= BrInx[UPCNInx-1]+1}
WendN= BrInx[UPCNInx+1]
WstartO2= BrInx[UPCNInx]+1
WendO1= BrInx[UPCNInx]; WendO2= BrInx[UPCNInx+1];
RSN=RegionPartL (RD,RDsq, WstartN , WendN ,CNR= CNRT,MeanF,BetaF,AlphaF,KappaF)
RSO=RegionPartL (RD,RDsq, WstartO1 , WendO1 ,CNR= CNRUp[UPCNInx],MeanF,BetaF,AlphaF,KappaF)+RegionPartL (RD,RDsq, WstartO2 , WendO2 ,CNR= CNRUp[UPCNInx+1],MeanF,BetaF,AlphaF,KappaF)
if( (CNRTC==1)&&( is.na(match(0,CNRUp[UPCNInx+2]))==T)){TranP= -log(GroupN-2)}
if( (CNRTC==2)&&( is.na(match(0,CNRUp[UPCNInx-1]))==T)){TranP= -log(GroupN-2)}
if( (CNRTC==1)&&( is.na(match(0,CNRUp[UPCNInx+2]))==F)){TranP= -log(GroupN-1)}
if( (CNRTC==2)&&( is.na(match(0,CNRUp[UPCNInx-1]))==F)){TranP= -log(GroupN-1)}
DecPro=exp(GSN+WSN+RSN- GSO-WSO-RSO+log(1- LambdaF)-log(LambdaF)+TranP)
DecPro
}
#Double Merge
if( ((UPCNInx==1)& (is.na(match(CNRT,CNRUp[UPCNInx+2]))==F)) | ((UPCNInx>1)& (is.na(match(CNRT,c(CNRUp[UPCNInx-1],CNRUp[UPCNInx+2])))==F)) ) {
# Form1
if(CNRTC==1){
print("DoubleMerge Form1")
CNRUpN=CNRUp;CNRUpN[UPCNInx]=CNRT;CNRUpN=CNRUpN[-((UPCNInx+1): (UPCNInx+2))]
BrInxN=BrInx[-( (UPCNInx) : (UPCNInx+1))]
WSN=WeightPartL(WeightIni,WeightUp, CNRUpN,GroupN, CountMatrix= as.matrix(CountC(CNRUpN,GroupN)))
WSO=WeightPartL(WeightIni,WeightUp, CNRUp,GroupN, CountMatrix= as.matrix(CountC(CNRUp,GroupN)))
GSN= GroupPartLog[CNRT]
GSO=sum(GroupPartLog[c(CNRUp[UPCNInx], CNRUp[UPCNInx+1], CNRUp[UPCNInx+2])])
if(UPCNInx==1){WstartN=1;WstartO1=1}
if(UPCNInx>1){WstartN=BrInx[UPCNInx-1]+1; WstartO1= BrInx[UPCNInx-1]+1}
WendN= BrInx[UPCNInx+2]
WstartO2= BrInx[UPCNInx]+1; WstartO3= BrInx[UPCNInx+1]+1;
WendO1= BrInx[UPCNInx]; WendO2= BrInx[UPCNInx+1]; WendO3= BrInx[UPCNInx+2]
RSN=RegionPartL (RD,RDsq, WstartN , WendN ,CNR= CNRT,MeanF,BetaF,AlphaF,KappaF)
RSO=RegionPartL (RD,RDsq, WstartO1 , WendO1 ,CNR= CNRUp[UPCNInx],MeanF,BetaF,AlphaF,KappaF)+RegionPartL (RD,RDsq, WstartO2 , WendO2 ,CNR= CNRUp[UPCNInx+1],MeanF,BetaF,AlphaF,KappaF) +RegionPartL (RD,RDsq, WstartO3 , WendO3 ,CNR=CNRUp[UPCNInx+2],MeanF,BetaF,AlphaF,KappaF)
if(is.na(match(0,CNRUp[length(CNRUp)]))==F){TL=1}
if(is.na(match(0,CNRUp[length(CNRUp)]))==T){TL=0}
if(is.na(match(0,CNRUp[1]))==F){T1=1}
if(is.na(match(0,CNRUp[1]))==T){T1=0}
TranP =(length(RD)-2-rowSums(CountC(CNRUpN,GroupN))[GroupN+1]-length(which(is.na(RD)==T))+T1+TL)*4/(GroupN-1)
DecPro=exp(GSN+WSN+RSN- GSO-WSO-RSO+2*log(1- LambdaF)-2*log(LambdaF)+log(TranP))
}
# Form2
if(CNRTC==2){
print("DoubleMerge Form2")
CNRUpN=CNRUp;CNRUpN[UPCNInx-1]=CNRT;CNRUpN=CNRUpN[-((UPCNInx): (UPCNInx+1))]
BrInxN=BrInx[-((UPCNInx-1): (UPCNInx))]
WSN=WeightPartL(WeightIni,WeightUp, CNRUpN,GroupN, CountMatrix= as.matrix(CountC(CNRUpN,GroupN)))
WSO=WeightPartL(WeightIni,WeightUp, CNRUp,GroupN, CountMatrix= as.matrix(CountC(CNRUp,GroupN)))
GSN= GroupPartLog[CNRT]
GSO=sum(GroupPartLog[c(CNRUp[UPCNInx-1], CNRUp[UPCNInx], CNRUp[UPCNInx+1])])
if((UPCNInx-1)==1){WstartN=1;WstartO1=1}
if((UPCNInx-1)>1){WstartN=BrInx[UPCNInx-2]+1; WstartO1= BrInx[UPCNInx-2]+1}
WendN= BrInx[UPCNInx+1]
WstartO2= BrInx[UPCNInx-1]+1; WstartO3= BrInx[UPCNInx]+1;
WendO1= BrInx[UPCNInx-1]; WendO2= BrInx[UPCNInx]; WendO3= BrInx[UPCNInx+1]
RSN=RegionPartL (RD,RDsq, WstartN , WendN ,CNR= CNRT,MeanF,BetaF,AlphaF,KappaF)
RSO=RegionPartL (RD,RDsq, WstartO1 , WendO1 ,CNR= CNRUp[UPCNInx-1],MeanF,BetaF,AlphaF,KappaF)+RegionPartL (RD,RDsq, WstartO2 , WendO2 ,CNR= CNRUp[UPCNInx],MeanF,BetaF,AlphaF,KappaF) +RegionPartL (RD,RDsq, WstartO3 , WendO3 ,CNR=CNRUp[UPCNInx+1],MeanF,BetaF,AlphaF,KappaF)
if(is.na(match(0,CNRUp[length(CNRUp)]))==F){TL=1}
if(is.na(match(0,CNRUp[length(CNRUp)]))==T){TL=0}
if(is.na(match(0,CNRUp[1]))==F){T1=1}
if(is.na(match(0,CNRUp[1]))==T){T1=0}
TranP =4/((GroupN-1)*(length(RD)-2-rowSums(CountC(CNRUpN,GroupN))[GroupN+1]-length(which(is.na(RD)==T))+T1+TL))
DecPro=exp(GSN+WSN+RSN- GSO-WSO-RSO+2*log(1- LambdaF) -2*log(LambdaF)+ log(TranP))
}
}
}
#if(is.na(DecPro)==T){DecPro=0}
MAccp=rbinom(1,1,min(1, DecPro))
if (MAccp==1){
return(list("Type"= "Merge","Result"="Success", "CNRUpN"=CNRUpN,"BrInxN" =BrInxN, "CNRO "= CNRUp, "BrInxO" =BrInx))
}
if (MAccp==0){
return(list("Type"="Merge" ,"Result"="Fail" , "CNRUpN"=CNRUp,"BrInxN" =BrInx, "CNRO"= CNRUp,"BrInxO" =BrInx))
}
}
# split
Spt<-function(RD, RDsq, GroupN,MeanF, BetaF,AlphaF,KappaF,LambdaF, WeightIni,WeightUp, GroupPartLog,CNRUp,BrInx,GroupCNV,BrFix,CNRUpBr){
BrInxO=BrInx[-(match(BrFix,BrInx))]
CNDiff=rep(0,(length(CNRUp)))
if(length(CNRUp)>1){
for (i in 2: (length(CNRUp))){
CNDiff[i]=BrInx[i]-BrInx[i-1] }
}
CNDiff[1]= BrInx[1]
DecPro =0
if(length(which((CNDiff>1)&(CNRUp!=0)))==0 ){DecPro=0}
if(length(which((CNDiff>1)&(CNRUp!=0)))>0 ){
if(length(which((CNDiff>1)&(CNRUp!=0)))==1 ){SptReg= which((CNDiff>1)&(CNRUp!=0))}
if(length(which((CNDiff>1)&(CNRUp!=0)))>1 ){
SptReg=sample(which((CNDiff>1)&(CNRUp!=0)) ,1)}
if(SptReg==1){CPoint=sample(c(1: (BrInx[1]-1)),1)}
if(SptReg!=1){
if( (BrInx[SptReg-1]+1)== (BrInx[SptReg]-1) ){CPoint= (BrInx[SptReg-1]+1)}
if( (BrInx[SptReg-1]+1)!= (BrInx[SptReg]-1) ){
CPoint=sample(c( (BrInx[SptReg-1]+1): (BrInx[SptReg]-1) ),1)
}
}
ChangInx=which((CNRUpBr[,1]<CPoint) &(CNRUpBr[,2]>CPoint))
BrInxON=sort(c(BrInxO,CPoint))
BrInxN= sort(c(BrInx,CPoint))
#Region
UPCNInx=which(BrInxN==CPoint)
CNRUpN=rep(NA,length(CNRUp)+1)
if(UPCNInx>1){CNRUpN[1: (UPCNInx-1)]=CNRUp[1: (UPCNInx-1)]}
if(UPCNInx<(length(CNRUpN)-1)){CNRUpN[(UPCNInx+2): (length(CNRUpN))]=CNRUp[(UPCNInx+1): (length(CNRUp))]}
CNRTC=sample(c(1,2),1)
CNRT=CNRUp[UPCNInx]
if(CNRTC==1){
CNRUpN[UPCNInx]= CNRUp [UPCNInx]
if(UPCNInx<(length(CNRUpN)-1)){
CNRUpN[UPCNInx+1]=sample(GroupCNV[-(which ( (GroupCNV==CNRUpN[UPCNInx+2]) | (GroupCNV==CNRUpN[UPCNInx])))] ,1)
}
if(UPCNInx==(length(CNRUpN)-1)){
CNRUpN[UPCNInx+1]=sample(GroupCNV[-(which ( (GroupCNV==CNRUpN[UPCNInx])))] ,1)
}
}
if(CNRTC==2){
CNRUpN[UPCNInx+1]= CNRUp [UPCNInx]
if(UPCNInx>1){
CNRUpN[UPCNInx]=sample(GroupCNV[-(which ( (GroupCNV==CNRUpN[UPCNInx+1]) | (GroupCNV==CNRUpN[UPCNInx-1])))] ,1)
}
if(UPCNInx==1){
CNRUpN[UPCNInx]=sample(GroupCNV[-(which ( (GroupCNV==CNRUp[1])))] ,1)
}
}
WSN=WeightPartL(WeightIni,WeightUp, CNRUpN,GroupN, CountMatrix= as.matrix(CountC(CNRUpN,GroupN)))
WSO=WeightPartL(WeightIni,WeightUp, CNRUp,GroupN, CountMatrix= as.matrix(CountC(CNRUp,GroupN)))
GSO= GroupPartLog[CNRT]
GSN=sum(GroupPartLog[c(CNRUpN[UPCNInx], CNRUpN[UPCNInx+1])])
if(UPCNInx==1){WstartN1=1;WstartO=1}
if(UPCNInx>1){WstartN1=BrInxN[UPCNInx-1]+1; WstartO= BrInx[UPCNInx-1]+1}
WstartN2= BrInxN[UPCNInx]+1
WendN1= BrInxN[UPCNInx]
WendN2= BrInxN[UPCNInx+1]
WendO= BrInx[UPCNInx]
RSO=RegionPartL (RD,RDsq, WstartO , WendO ,CNR= CNRT,MeanF,BetaF,AlphaF,KappaF)
RSN=RegionPartL (RD,RDsq, WstartN1 , WendN1 ,CNR= CNRUpN[UPCNInx],MeanF,BetaF,AlphaF,KappaF)+RegionPartL (RD,RDsq, WstartN2 , WendN2 ,CNR= CNRUpN[UPCNInx+1],MeanF,BetaF,AlphaF,KappaF)
if( (CNRTC==1)&&( is.na(match(0,CNRUp[UPCNInx+2]))==T)){TranP= log(GroupN-2)}
if( (CNRTC==2)&&( is.na(match(0,CNRUp[UPCNInx-1]))==T)){TranP= log(GroupN-2)}
if( (CNRTC==1)&&( is.na(match(0,CNRUp[UPCNInx+2]))==F)){TranP= log(GroupN-1)}
if( (CNRTC==2)&&( is.na(match(0,CNRUp[UPCNInx-1]))==F)){TranP= log(GroupN-1)}
DecPro=exp(GSN+WSN+RSN- GSO-WSO-RSO-log(1- LambdaF)+log(LambdaF)+TranP)
}
if(is.na(DecPro)==T){DecPro=0}
MAccp=rbinom(1,1,min(1, DecPro))
if (MAccp==1){
return(list("Type"= "Split","Result"="Success", "CNRUpN"=CNRUpN,"BrInxN" =BrInxN, "CNRO "= CNRUp, "BrInxO" =BrInx))
}
if (MAccp==0){
return(list("Type"="Split" ,"Result"="Fail" , "CNRUpN"=CNRUp,"BrInxN" =BrInx, "CNRO"= CNRUp,"BrInxO" =BrInx))
}
}
### Step 4.3Double Split
DBSpt<-function(RD, RDsq, GroupN,MeanF, BetaF,AlphaF,KappaF,LambdaF, WeightIni,WeightUp, GroupPartLog,CNRUp,BrInx,GroupCNV,BrFix,CNRUpBr){
BrInxO=BrInx[-(match(BrFix,BrInx))]
CNDiff=rep(0,(length(CNRUp)))
if(length(CNRUp)>1){
for (i in 2: (length(CNRUp))){
CNDiff[i]=BrInx[i]-BrInx[i-1] }
}
CNDiff[1]= BrInx[1]
DecPro =0
if( length(which((CNDiff>2)&(CNRUp!=0))) ==0 ){ DecPro =0}
if( length(which((CNDiff>2)&(CNRUp!=0))) >0 ){
if( length(which((CNDiff>2)&(CNRUp!=0))) ==1 ){ SptReg= which((CNDiff>2)&(CNRUp!=0))}
if( length(which((CNDiff>2)&(CNRUp!=0))) >1 ){
SptReg=sample(which((CNDiff>2)&(CNRUp!=0)) ,1) }
if(SptReg==1){CPoint=sort(sample(c(1: (BrInx[1]-1)),2))}
if(SptReg!=1) {CPoint=sort(sample(c( (BrInx[SptReg-1]+1): (BrInx[SptReg]-1) ),2))}
ChangInx=which((CNRUpBr[,1]<CPoint) &(CNRUpBr[,2]>CPoint))
BrInxON=sort(c(BrInxO,CPoint))
BrInxN= sort(c(BrInx,CPoint))
UPCNInx= match(CPoint,BrInxN)
CNRUpN=rep(NA,length(CNRUp)+2)
if(UPCNInx[1]>1){CNRUpN[1: (UPCNInx[1]-1)]=CNRUp[1: (UPCNInx[1]-1)]}
if(UPCNInx[1]<(length(CNRUpN)-2)){CNRUpN[(UPCNInx[1]+3): (length(CNRUpN))]=CNRUp[(UPCNInx[1]+1): (length(CNRUp))]}
CNRUpN[UPCNInx[1]]=CNRUp[UPCNInx[1]]
CNRUpN[UPCNInx[1]+2]=CNRUp[UPCNInx[1]]
CNRUpN[UPCNInx[1]+1]=sample(GroupCNV[-(which ( (GroupCNV== CNRUp[UPCNInx[1]])))] ,1)
WSN=WeightPartL(WeightIni,WeightUp, CNRUpN,GroupN, CountMatrix= as.matrix(CountC(CNRUpN,GroupN)))
WSO=WeightPartL(WeightIni,WeightUp, CNRUp,GroupN, CountMatrix= as.matrix(CountC(CNRUp,GroupN)))
GSN=sum( GroupPartLog[c(CNRUpN[UPCNInx[1]], CNRUpN[UPCNInx[1]+1], CNRUpN[UPCNInx[1]+2] ) ])
GSO=(GroupPartLog[CNRUpN[UPCNInx[1]]])
if((UPCNInx[1])==1){WstartN1=1;WstartO=1}
if((UPCNInx[1])>1){WstartN1=BrInx[UPCNInx[1]-1]+1; WstartO= BrInxN[UPCNInx[1]-1]+1}