Nothing
hap.freq<-function(geno){
n.poly<-ncol(geno)/2
pM<-allele.freq(geno)
pMd<-array(NA,c(n.poly,n.poly))
pMd.lb<-array(NA,dim=c(n.poly,n.poly))
pMd.ub<-array(NA,dim=c(n.poly,n.poly))
for (i in 1:(n.poly-1)){
for (j in (i+1):n.poly){
geno.t<-cbind(geno[,(2*i-1):(2*i)],geno[,(2*j-1):(2*j)])
temp<-haplo.em(geno.t)
if (nrow(as.matrix(temp$hap.prob))==4){
pMd[i,j]<-temp$hap.prob[1]
pMd[j,i]<-temp$hap.prob[1]
}
if (nrow(as.matrix(temp$hap.prob))<4){
a<-sort(unique.default(c(geno[,(2*i-1)],geno[,(2*i)])))
b<-sort(unique.default(c(geno[,(2*j-1)],geno[,(2*j)])))
if (temp$haplotype[1,1]==a[1] && temp$haplotype[1,2]==b[1]){
pMd[i,j]<-temp$hap.prob[1]
pMd[j,i]<-temp$hap.prob[1]
}
else {
pMd[i,j]<-0
pMd[j,i]<-0
}
}
}
}
pMd
}
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