EM computation of haplotype frequencies with two SNPs. The computation is relied on the package"haplo.stats".
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 ncol(geno) = 2*K. Rows represent the alleles for each subject. Each allele shoud be represented as numbers (A=1,C=2,G=3,T=4).
matrix of haplotype frequencies consisted of two alleles from each SNP. These alleles are the same ones computed for frequency using the function "allele.freq".
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