Nothing
"extractA"<-function(G,marker.type="MSW"){
if(is.genotype(G[[1]])==FALSE & is.genotypeD(G[[1]])==FALSE){
if("id"%in%colnames(G)){
G<-G[,-which(colnames(G)=="id")]
}
if("categories"%in%colnames(G)){
G<-G[,-which(colnames(G)=="categories")]
}
G<-genotype.list(G,marker.type=marker.type)
}
A<-lapply(G, function(x){summary(x)$allele.freq[,"Proportion"][1:nallele(x)]})
if(marker.type=="AFLP" | is.genotypeD(G[[1]])){
A<-lapply(A, function(x){
if(any(x==1)){
warning("some loci are monomorphic: setting allele frequencies to 0.9999 and 0.0001")
x[which(x==1)]<-0.9999
x[which(x==0)]<-0.0001
}else{
x<-x
}
x
})
}
A
}
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