Provide a summary of missing allele information for each individual in the genotype matrix. The number of loci missing zero, one, or two alleles is computed, as well as the total number of haplotype pairs that could result from the observed phenotype.
Matrix of alleles, such that each locus has a pair of adjacent columns of alleles, and the order of columns corresponds to the order of loci on a chromosome. If there are K loci, then geno has 2*K columns. Rows represent all observed alleles for each subject.
Vector of codes for allele missing values.
After getting information on the individual loci, this function makes a call to geno.count.pairs(). The E-M steps to estimate haplotype frequencies considers haplotypes that could result from a phenotype with a missing allele. It will not remove a subject's phenotype, only the unlikely haplotypes that result from it.
Data frame with columns representing the number of loci with zero, one, and two missing alleles, then the total haplotype pairs resulting from full enumeration of the phenotype.