Nothing
lrtG<-function(n.fp,genoT,genoC){ ## true order
n<-ncol(genoC)
ncon<-ncol(genoT)
n.poly<-nrow(genoT)
choices<-0
for(i in 1:n.fp) choices<-choices+choose(n.poly,i)
af<-allele.freq.G(genoT)
caf<-allele.freq.G(genoC)
genoT[which(af>caf),][genoT[which(af>caf),]==1]<-2
genoT[which(af>caf),][genoT[which(af>caf),]==0]<-1
genoT[which(af>caf),][genoT[which(af>caf),]==2]<-0
genoC[which(af>caf),][genoC[which(af>caf),]==1]<-2
genoC[which(af>caf),][genoC[which(af>caf),]==0]<-1
genoC[which(af>caf),][genoC[which(af>caf),]==2]<-0
temp<-.C("LRT",as.integer(n.fp),as.integer(n.poly),as.integer(as.vector( as.vector(t(as.matrix(genoT))))),as.integer( as.vector(t(as.matrix(genoC)))),as.integer(ncon),as.integer(n[1]/2),pMMcV=double(choices),df=double(choices))
lr2<-temp$pMMcV[1:choices]
df<-temp$df
rm(temp)
info<-array(NA,c(choices,n.fp))
id<-1
for(j in 1:n.fp){
no<-1:j
no.t<-no
for (i in 1:choose(n.poly,j)){
info[id,1:j]<-no.t
id<-id+1
z<-sum(no.t==n.poly-j+no)
if (z!=j) {
no.t[j-z]<-no.t[j-z]+1
if (z>0) for (j in (j-z+1):j) no.t[j]<-no.t[j-1]+1
}
}
}
gc()
cbind(1:choices,info,pchisq((lr2),df),lr2, df)
}
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