GAPIT.Genotype.R

`GAPIT.Genotype` <-
function(G=NULL,GD=NULL,GM=NULL,KI=NULL,
  kinship.algorithm=NULL,SNP.effect="Add",SNP.impute="Middle",PCA.total=0,seed=123, SNP.fraction =1,
  file.path=NULL,file.from=NULL, file.to=NULL, file.total=NULL, file.fragment = 1000,SNP.test=TRUE,
  file.G =NULL,file.Ext.G =NULL,
  file.GD=NULL,file.Ext.GD=NULL,
  file.GM=NULL,file.Ext.GM=NULL,
  SNP.MAF=0.05,FDR.Rate = 0.05,SNP.FDR=1,
  Timmer=NULL,Memory=NULL,
  LD.chromosome=NULL,LD.location=NULL,LD.range=NULL, SNP.CV=NULL,
  GP = NULL,GK = NULL,GTindex=NULL,  
  bin.size = 1000,inclosure.size = 100,
  sangwich.top=NULL,sangwich.bottom=NULL,
  file.output=TRUE,
  Create.indicator = FALSE, Major.allele.zero = FALSE,Geno.View.output=TRUE){
#Object: To unify genotype and calculate kinship and PC if required:
#       1.For G data, convert it to GD and GI
#       2.For GD and GM data, nothing change 
#       3.Samling GD and create KI and PC
#       4.Go through multiple files
#       5.In any case, GD must be returned (for QC)
#Output: GD, GI, GT, KI and PC
#Authors: Zhiwu Zhang
#Last update: August 11, 2011
##############################################################################################

#print("Genotyping: numericalization, sampling kinship, PCs and much more...")



Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype start")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype start")

#Create logical variables
byData=!is.null(G) | !is.null(GD)
byFile=!is.null(file.G) | !is.null(file.GD)
hasGenotype=(byData | byFile  )
needKinPC=(is.null(KI) | PCA.total>0 | kinship.algorithm=="Separation")

if(!is.null(KI) & !byData & !byFile & !SNP.test &kinship.algorithm!="SUPER") {
print("It return unexpected")
return (list(GD=NULL,GI=NULL,GT=NULL,hasGenotype=FALSE, genoFormat=NULL, KI=KI,PC=NULL,byFile=FALSE,fullGD=TRUE,Timmer=Timmer,Memory=Memory))
}


#Set indicator for full GD
fullGD=FALSE
if(byData) fullGD=TRUE
if(byFile & SNP.fraction==1 & needKinPC) fullGD=TRUE

#SET GT to NULL in case of no genotype
if(!byData & !byFile & is.null(GK) &kinship.algorithm!="SUPER") {
if(is.null(KI) & is.null(GP) & is.null(GK)) stop("GAPIT says: Kinship has to be provided or estimated from genotype!!!")
return (list(GD=NULL,GI=NULL,GT=NULL,hasGenotype=FALSE, genoFormat=NULL, KI=KI,PC=NULL,byFile=FALSE,fullGD=TRUE,Timmer=Timmer,Memory=Memory))
}

genoFormat="hapmap"
if(is.null(G)&is.null(file.G)) genoFormat="EMMA"

#Multiple genotype files

#In one of the 3 situations, calculate KI with the algorithm specified, otherwise skip cit by setting algorithm to "SUPER"
kinship.algorithm.save=kinship.algorithm
kinship.algorithm="SUPER"
#Normal
if(is.null(sangwich.top) & is.null(sangwich.bottom) ) kinship.algorithm=kinship.algorithm.save

#TOP or Bottom is MLM
pass.top=FALSE
if(!is.null(sangwich.top))   pass.top=!(sangwich.top=="FaST" | sangwich.top=="SUPER" | sangwich.top=="DC")
pass.bottom=FALSE
if(!is.null(sangwich.bottom))   pass.bottom=!(sangwich.bottom=="FaST" | sangwich.bottom=="SUPER" | sangwich.bottom=="DC")

if(pass.top | pass.bottom )kinship.algorithm=kinship.algorithm.save



#Compatibility of input

#agreement among file from, to and total
if(!is.null(file.from) &!is.null(file.to) &!is.null(file.total)){
if(file.total!=(file.to-file.from+1))  stop("GAPIT says: Conflict among file (from, to and total)")
}
if(!is.null(file.from) &!is.null(file.to)) {
  if(file.to<file.from)  stop("GAPIT says: file.from should smaller than file.to")
}
#file.from and file.to must be in pair
if(is.null(file.from) &!is.null(file.to) ) stop("GAPIT says: file.from and file.to must be in pair)")
if(!is.null(file.from) &is.null(file.to) ) stop("GAPIT says: file.from and file.to must be in pair)")

#assign file.total
if(!is.null(file.from) &!is.null(file.to) ) file.total=file.to-file.from+1
if(byFile& is.null(file.total)) stop("GAPIT says: file.from and file.to must be provided!)")

if(!is.null(GP) & !is.null(GK) ) stop("GAPIT Says: You can not provide GP and GK at same time")
if(!is.null(GP) & !is.null(KI) ) stop("GAPIT Says: You can not provide GP and KI at same time")
if(!is.null(GK) & !is.null(KI))   stop("GAPIT says: You can not specify GK and KI at same time!!!")

#GP does not allow TOP
if(!is.null(GP) & !is.null(sangwich.top) ) stop("GAPIT Says: You provided GP. You can not spycify sangwich.top")

#Top require a bottom
if(!is.null(sangwich.top) & is.null(sangwich.bottom) ) stop("GAPIT Says: Top require its Bottom")

#naked bottom require GP or GK
if(is.null(sangwich.top) & !is.null(sangwich.bottom) & (is.null(GP) & is.null(GK)) ) stop("GAPIT Says: Uncovered Bottom (without TOP) requires GP or GK")

#Pseudo top (GK or GP) requires a bottom
if(is.null(sangwich.top) & is.null(sangwich.bottom) & (!is.null(GP)|!is.null(GK  ))) stop("GAPIT Says: You have provide GP or GK, you need to provide Bottom")

#if(!is.null(KI) &!is.null(kinship.algorithm))  stop("GAPIT says: You can not specify kinship.algorithm and provide kinship at same time!!!")



if(!needKinPC &SNP.fraction<1)  stop("GAPIT says: You did not require calculate kinship or PCs. SNP.fraction should not be specified!!!")
if(!SNP.test & is.null(KI) & !byData & !byFile)  stop("GAPIT says: For SNP.test optioin, please input either use KI or use genotype")

#if(is.null(file.path) & !byData & byFile) stop("GAPIT Ssays: A path for genotype data should be provided!")
if(is.null(file.total) & !byData & byFile) stop("GAPIT Ssays: Number of file should be provided: >=1")
if(!is.null(G) & !is.null(GD)) stop("GAPIT Ssays: Both hapmap and EMMA format exist, choose one only.")

if(!is.null(file.GD) & is.null(file.GM) & (!is.null(GP)|!is.null(GK)) ) stop("GAPIT Ssays: Genotype data and map files should be in pair")
if(is.null(file.GD) & !is.null(file.GM) & (!is.null(GP)|!is.null(GK)) ) stop("GAPIT Ssays: Genotype data and map files should be in pair")

if(!is.null(GD) & is.null(GM) & (is.null(GP)&is.null(GK)) &kinship.algorithm!="SUPER") stop("GAPIT Says: Genotype data and map files should be in pair")
if(is.null(GD) & !is.null(GM) & (is.null(GP)&is.null(GK)) &kinship.algorithm!="SUPER") stop("GAPIT Says: Genotype data and map files should be in pair")


#if(!byData & !byFile) stop("APIT Ssays: Either genotype data or files should be given!")
#if(byData&(!is.null(file.path))) stop ("APIT Ssays: You have provided geotype data. file.path should not be provided!")

#print("Pass compatibility of input")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype loaded")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype loaded")
  
#Inital GLD
GLD=NULL
SNP.QTN=NULL #Intitial
GT=NULL

#Handler of read data in numeric format (EMMA)
#Rename GM as GI
if(!is.null(GM))GI=GM
rm(GM)
gc()
#Extract GD and GT from read data GD
if(!is.null(GD) )
{
GT=as.matrix(GD[,1])  #get taxa
GD=as.matrix(GD[,-1]) #remove taxa column
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GT created from GD)")
Memory=GAPIT.Memory(Memory=Memory,Infor="GT created from GD")
}

#Hapmap format
if(!is.null(G))
{

Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before HapMap")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before HapMap")

#Convert HapMap to numerical
print(paste("Converting genotype...",sep=""))


hm=GAPIT.HapMap(G,SNP.effect=SNP.effect,SNP.impute=SNP.impute, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)

Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="after HapMap")
Memory=GAPIT.Memory(Memory=Memory,Infor="after HapMap")


#Extracting SNP for LD plot
if(!is.null(LD.chromosome)){
#print("Extracting SNP for LD plot...")
  chromosome=(G[,3]==LD.chromosome[1])
  bp=as.numeric(as.vector(G[,4]))
  deviation=abs(bp-as.numeric(as.vector(LD.location[1])) )
  location=deviation< as.numeric(as.vector(LD.range[1])  )
  index=chromosome&location
  GLD=G[index,]

}else{
#print("No data in GLD")
  GLD=NULL
}

Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="HapMap")
Memory=GAPIT.Memory(Memory=Memory,Infor="HapMap")
print(paste("Converting genotype done.",sep=""))
#rm(G)
#gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="G removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="G removed")

GT=hm$GT
GD=hm$GD
GI=hm$GI


rm(hm)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="hm removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="hm removed")
}

#From files
if(!byData & byFile){
#print("Loading genotype from files...")

Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="byFile")
Memory=GAPIT.Memory(Memory=Memory,Infor="byFile")

  numFileUsed=file.to
  if(!needKinPC)numFileUsed=file.from

  #Initial GI as storage
  GD=NULL
  GT=NULL
  GI=NULL
  GLD=NULL

  #multiple fragments or files
  for (file in file.from:numFileUsed){

    frag=1
    numSNP=file.fragment
    myFRG=NULL
   #print(paste("numSNP  before while is ",numSNP))

    while(numSNP==file.fragment) {     #this is problematic if the read end at the last line
    print(paste("Reading file: ",file,"Fragment: ",frag))

Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before Fragment")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before Fragment")
    
      myFRG=GAPIT.Fragment( file.path=file.path,file.from=file.from, file.to=file.to,file.total=file.total,file.G=file.G,file.Ext.G=file.Ext.G,
                            seed=seed,SNP.fraction=SNP.fraction,SNP.effect=SNP.effect,SNP.impute=SNP.impute,genoFormat=genoFormat,
                            file.GD=file.GD,file.Ext.GD=file.Ext.GD,file.GM=file.GM,file.Ext.GM=file.Ext.GM,
                            file.fragment=file.fragment,file=file,frag=frag,
                            LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
   #print(paste("numSNP after while is ",numSNP))
     #print(paste("OK with file: ",file,"Fragment: ",frag))

     Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="After Fragment")
     Memory=GAPIT.Memory(Memory=Memory,Infor="After Fragment")


      if(is.null(GT) & !is.null(myFRG$GT))GT= as.matrix(myFRG$GT)

      if(is.null(GD)){
        GD= myFRG$GD
      }else{
        if(!is.null(myFRG$GD))    {
          GD=cbind(GD,myFRG$GD)
        }
      }

      if(is.null(GI)){
        GI= myFRG$GI
      }else{
        if(!is.null(myFRG$GI))    {
          colnames(myFRG$GI)=c("SNP","Chromosome","Position")
          GI=as.data.frame(rbind(as.matrix(GI),as.matrix(myFRG$GI)))
        }
      }

      if(is.null(G)){
        G= myFRG$G
      }else{
        if(!is.null(myFRG$G))    {
          G=as.data.frame(rbind(as.matrix(G),as.matrix(myFRG$G[-1,])))
        }
      }
      
      if(is.null(GLD)){
        GLD= myFRG$GLD
      }else{
        if(!is.null(myFRG$GLD))    {
          if(myFRG$heading){
          GLD=as.data.frame(rbind(as.matrix(GLD),as.matrix(myFRG$GLD[-1,])))
          }else{
          GLD=as.data.frame(rbind(as.matrix(GLD),as.matrix(myFRG$GLD)))
          }
        }
      }

      #print("This fragment is joined")

      if(file==file.from & frag==1)GT=as.matrix(myFRG$GT)

      frag=frag+1
      if(!is.null(myFRG$GI))    {
        numSNP=myFRG$linesRead[1]
      }else{
       numSNP=0
      }

      if(!needKinPC)numSNP=0  #force to end the while loop
      if(is.null(myFRG))numSNP=0  #force to end the while loop

     Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="END this Fragment")
     Memory=GAPIT.Memory(Memory=Memory,Infor="END this Fragment")



    } #end of repeat on fragment
   # print("This file is OK")
  } #end of file loop
  print("All files loaded")
} #end of if(!byData&byFile)


#print("file loaded")

Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Sampling genotype")
Memory=GAPIT.Memory(Memory=Memory,Infor="Sampling genotype")

#Plot thirt part kinship
if(!is.null(KI) &file.output) {
if(KI!=1) {



  if(nrow(KI)<1000){
    print("Plotting Kinship")
    
    theKin=as.matrix(KI[,-1])
    colnames(theKin)=KI[,1]
    rownames(theKin)=KI[,1]

Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="set kinship")
Memory=GAPIT.Memory(Memory=Memory,Infor="set kinship")

    print("Creating heat map for kinship...")
    pdf(paste("GAPIT.Kin.thirdPart.pdf",sep=""), width = 12, height = 12)
    par(mar = c(25,25,25,25))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="prepare heatmap")
Memory=GAPIT.Memory(Memory=Memory,Infor="prepare heatmap")
    
    heatmap.2(theKin,  cexRow =.2, cexCol = 0.2, col=rev(heat.colors(256)), scale="none", symkey=FALSE, trace="none")
    dev.off()
    print("Kinship heat map PDF created!")
    
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="plot heatmap")
Memory=GAPIT.Memory(Memory=Memory,Infor="plot heatmap")

    
  } #end of if(nrow(KI)<1000)
} #end of if(KI!=1)
} #end of if(!is.null(KI))

Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before SUPER")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before SUPER")

#SUPER
if(!is.null(GP) & kinship.algorithm=="SUPER" & !is.null(bin.size) & !is.null(inclosure.size)){
  mySpecify=GAPIT.Specify(GI=GI,GP=GP,bin.size=bin.size,inclosure.size=inclosure.size)
  SNP.QTN=mySpecify$index
  
  if(!is.null(GD)){
	#comment out to keep all taxa for GS, Zhiwu (Dec7, 2012)
    #GK=GD[GTindex,SNP.QTN] 
    #SNPVar=apply(as.matrix(GK),2,var)
    #GK=GK[,SNPVar>0]
    #GK=cbind(as.data.frame(GT[GTindex]),as.data.frame(GK)) #add taxa  

	GK=GD[,SNP.QTN]
    SNPVar=apply(as.matrix(GK),2,var)
    GK=GK[,SNPVar>0]
    GK=cbind(as.data.frame(GT),as.data.frame(GK)) #add taxa  

    	
		
		#print("QTN extracted")  
  }

  
}


Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before PCA")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before PCA")

#Create PC
PC=NULL
thePCA=NULL
if(PCA.total>0 | kinship.algorithm=="Separation"){
thePCA=GAPIT.PCA(X = GD, taxa = GT, PC.number = PCA.total,file.output=file.output,PCA.total=PCA.total)
PC=thePCA$PCs[,1:(1+PCA.total)]
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PCA")
Memory=GAPIT.Memory(Memory=Memory,Infor="PCA")
print("PC created")
}

Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before creating kinship")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before creating kinship")


#Create kinship from genotype if not provide
if(is.null(KI) & (!is.null(GD) |!is.null(GK)) & kinship.algorithm!="SUPER")
{
  print("Calculating kinship...")
  
  if(!is.null(GK)){
    thisGD=GK[,-1]
    myGT=as.matrix(GK[,1])
    print("GK is used to create KI")
  }else{
    thisGD=GD
    myGT=GT

	#comment out to keep all taxa for GS, Zhiwu (Dec7, 2012)
    #if(!is.null(GTindex)){
    #  thisGD=thisGD[GTindex,]    
    #  myGT=myGT[GTindex]    
    #}
  }
  
 print(paste("Number of individuals and SNPs are ",nrow(thisGD)," and ",ncol(thisGD)))
 theKin=NULL

  if(kinship.algorithm=="EMMA"){
    half.thisGD = as.matrix(.5*thisGD)
    if(length(which(is.na(half.thisGD))) > 0){
      print("Substituting missing values with heterozygote for kinship matrrix calculation....")
      half.thisGD[which(is.na(half.thisGD))] = 1
    }
    theKin= emma.kinship(snps=t(as.matrix(.5*thisGD)), method="additive", use="all")
  }  
  if(kinship.algorithm=="Loiselle")theKin= GAPIT.kinship.loiselle(snps=t(as.matrix(.5*thisGD)), method="additive", use="all")
  if(kinship.algorithm=="VanRaden")theKin= GAPIT.kinship.VanRaden(snps=as.matrix(thisGD)) 
  if(kinship.algorithm=="Zhang")theKin= GAPIT.kinship.ZHANG(snps=as.matrix(thisGD)) 
  if(kinship.algorithm=="Separation")theKin= GAPIT.kinship.separation(PCs=thePCA$PCs,EV=thePCA$EV,nPCs=PCA.total)
 
if(!is.null(theKin)){ 
  colnames(theKin)=myGT
  rownames(theKin)=myGT
 print("kinship calculated")

  if(length(GT)<1000 &file.output){
    #Create heat map for kinship
    print("Creating heat map for kinship...")

    pdf(paste("GAPIT.Kin.",kinship.algorithm,".pdf",sep=""), width = 12, height = 12)
    par(mar = c(25,25,25,25))
    heatmap.2(theKin,  cexRow =.2, cexCol = 0.2, col=rev(heat.colors(256)), scale="none", symkey=FALSE, trace="none")
    dev.off()
    print("Kinship heat map created")
  }

  print("Adding IDs to kinship...")
  #Write the kinship into a text file
  KI=cbind(myGT,as.data.frame(theKin)) #This require big memory. Need a way to solve it.
  

  print("Writing kinship to file...")
  if(file.output) write.table(KI, paste("GAPIT.Kin.",kinship.algorithm,".csv",sep=""), quote = FALSE, sep = ",", row.names = FALSE,col.names = FALSE)
  print("Kinship save as file")

  rm(theKin)
  gc()
}
  Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Estimating kinship")
  Memory=GAPIT.Memory(Memory=Memory,Infor="Estimating kinship")
  print("Kinship created!")
}  #end of if(is.null(KI)&!is.null(GD))

Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="after creating kinship")
Memory=GAPIT.Memory(Memory=Memory,Infor="after creating kinship")

#LD plot
#print("LD section")
if(!is.null(GLD) &file.output){

if(nrow(GLD)>500){
  GLD=GLD[1,]
  print("WARNING: The number of SNPs requested is beyond limitation. No LD plot created.")
}
if(nrow(GLD)>1)
{
print("Plot LD...")

hapmapgeno= data.frame(as.matrix(t(GLD[,-c(1:11)])))

hapmapgeno[hapmapgeno=="NN"]=NA
hapmapgeno[hapmapgeno=="XX"]=NA
hapmapgeno[hapmapgeno=="--"]=NA
hapmapgeno[hapmapgeno=="++"]=NA
hapmapgeno[hapmapgeno=="//"]=NA

LDdist=as.numeric(as.vector(GLD[,4]))
LDsnpName=GLD[,1]
colnames(hapmapgeno)=LDsnpName

#Prune SNM names
#LDsnpName=LDsnpName[GAPIT.Pruning(LDdist,DPP=7)]
LDsnpName=LDsnpName[c(1,length(LDsnpName))] #keep the first and last snp names only

#print(hapmapgeno)
print("Getting genotype object")

LDsnp=makeGenotypes(hapmapgeno,sep="",method=as.genotype)   #This need to be converted to genotype object

print("Caling LDheatmap...")
pdf(paste("GAPIT.LD.chromosom",LD.chromosome,"(",round(max(0,LD.location-LD.range)/1000000),"_",round((LD.location+LD.range)/1000000),"Mb)",".pdf",sep=""), width = 12, height = 12)
#pdf(paste("GAPIT.LD.pdf",sep=""), width = 12, height = 12)
par(mar = c(25,25,25,25))
MyHeatmap <- try(LDheatmap(LDsnp, LDdist, LDmeasure="r", add.map=TRUE,
  SNP.name=LDsnpName,color=rev(cm.colors(20)), name="myLDgrob", add.key=TRUE,geneMapLabelY=0.1) )

if(!inherits(MyHeatmap, "try-error")) {
  #Modify the plot
  grid.edit(gPath("myLDgrob", "Key", "title"), gp=gpar(cex=.5, col="blue"))  #edit key title size and color
  grid.edit(gPath("myLDgrob", "geneMap", "title"), gp=gpar(just=c("center","bottom"), cex=0.8, col="black")) #Edit gene map title
  grid.edit(gPath("myLDgrob", "geneMap","SNPnames"), gp = gpar(cex=0.3,col="black")) #Edit SNP name
}else{
  print("Warning: error in converting genotype. No LD plot!")
}

dev.off()
print("LD heatmap crated")
#grid.edit(gPath("myLDgrob", "heatMap","title"), gp=gpar(cex=1.0))   #Make title smaler
#grid.edit(gPath("myLDgrob", "geneMap", "title"), gp=gpar(just=c("right","bottom"), cex=0.5, col="blue")) #Edit gene map title
#grid.edit(gPath("myLDgrob", "Key", "labels"), gp=gpar(cex=.5, col="black"))  #edit key lable size and color
}else{ # alternative of if(nrow(GLD)>1)
  print("Warning: There are less than two SNPs on the region you sepcified. No LD plot!")
} #end of #if(nrow(GLD)>1)
}#end of if(!is.null(GLD))

Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="after LD plot")
Memory=GAPIT.Memory(Memory=Memory,Infor="after LD plot")


###output Marker density and decade of linkage disequilibrium over distance
if(!is.null(GI) & !is.null(GD) & file.output & Geno.View.output){
ViewGenotype<-GAPIT.Genotype.View(
myGI=GI,
myGD=GD,
#chr=1,
#w1_start=30,
#w1_end=230,
#mav1=10
)
}





#print("Genotype successfully acomplished")
return (list(G=G,GD=GD,GI=GI,GT=GT,hasGenotype=hasGenotype, genoFormat=genoFormat, KI=KI,PC=PC,byFile=byFile,fullGD=fullGD,Timmer=Timmer,Memory=Memory,SNP.QTN=SNP.QTN))
}
#=============================================================================================