R/expectedGenotypes.R

In BayHap: Bayesian analysis of haplotype association using Markov Chain Monte Carlo

`expectedGenotypes` <-
function (x, alleles = allele.names(x), ploidy = 2, sort = TRUE, 
    haplotype = FALSE) 
{
    if (missing(x) && missing(alleles)) 
        stop("at least one of 'x' or 'alleles' must be given")
    if (!(missing(x) && !missing(alleles))) {
        if (!is.genotype(x)) 
            stop("x must be of class 'genotype'")
    }
    nA <- length(alleles)
    if (nA == 0) 
        stop("Zero length alleles vector.")
    if (sort) {
        allelesOrig <- alleles
        alleles <- paste(1:nA, alleles, sep = "")
    }
    if (!haplotype) {
        comb <- combinations(n = nA, r = ploidy, v = alleles, 
            repeats.allowed = T)
    }
    else {
        comb <- permutations(n = nA, r = ploidy, v = alleles, 
            repeats.allowed = T)
    }
    if (sort) {
        for (i in 1:nA) comb[comb == alleles[i]] <- allelesOrig[i]
    }
    nC <- dim(comb)
    ret <- vector(mode = "character", length = nC[1])
    ret <- paste(comb[, 1], comb[, 2], sep = "/")
    if (ploidy > 2) {
        for (i in 3:nC[2]) {
            ret <- paste(ret, comb[, i], sep = "/")
        }
    }
    return(ret)
}