Figure 4.

CNVice algorithm. h_k and h_q are alleles, where k and q represent the number of copies of a gene in each chromosome. The observed diploid copy number, or the total copy number, is denoted by j, where j = k + q, k and q being natural numbers. The population structure parameter is f (or f_CNV), and the probability of an allele to be k is p_k. For example, an individual with genotype (h₃, h₁) for a locus L has 3 copies of the allele in one chromosome, 1 copy on the other, and diploid copy number 4; the probability of the allele to be h₃ in the population is given by p₃ and of the allele h₁ is given by p₁. n is the total number of individuals in the sample, and g is the number of iterations. δ_it is a binary variable that indicates whether the t allele is present in genotype i = (h_k, h_q). Steps: E, expectation; M, maximization.