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. Author manuscript; available in PMC: 2015 Mar 23.
Published in final edited form as: Tissue Antigens. 2007 Apr;69(0 1):192–197. doi: 10.1111/j.1399-0039.2006.00769.x

Table 1.

Statistical functions, N/A: not applicable; HWP: Hardy-Weinberg proportions

Functions Notes References for function
Population summary Sample size (n); allele frequencies; number of distinct alleles per locus (k) N/A
Genotype summary Lower triangular matrix with observed and expected genotype counts; significant genotypes highlighted. N/A
χ2test of HWP χ2-square statistic; degrees of freedom; associated P-value for several classes of genotypes (e.g., all heterozygotes, all homozygotes, common genotypes) (17)
Exact test of HWP Three modules: Markov chain Monte Carlo version based on original Guo & Thompson code (4); a modified Monte-Carlo version (no Markov chain); a module that calls Arlequin (18). (4)
Ewens-Watterson test of neutrality Observed and expected homozygosity (F), its expected value, variance, and normalised deviate (Fnd) under neutrality Slatkin’s (5, 6) implementation (7, 8)(19)
Haplotype frequency estimation Haplotypes frequencies estimated using the expectation-maximization (EM) algorithm. (20, 21)
Linkage disequilibrium (LD) measures Significance tested by the permutation distribution of the likelihood-ratio statistic; Overall measures of multi-allelic LD: D′ and Wn (22) D′ (23); Wn (24)