Agglomerative haplotype analysis: testing for differences between two population samples' homozygous segment length distributions. We compared the homozygous segment length distributions between JPT and CHB at each locus position in the chromosome 20 masked ISLMcm matrix by calculating the Cramer-von Mises two-sample minimum distance statistic ω2. A representative position (Chr 20:43.82 Mb) with a high ω2 value was chosen to illustrate the AHA permutation testing procedure. (a) ω2 values between JPT and CHB for chromosome 20. (b) Segment length ECDFs for JPT and CHB at example peak ω2 position. (c) Determination of significance level using permutation test: ECDFs from 100,000 resamples after mixing JPT and CHB data and randomly reassigning group labels. ω2 was calculated for each permutation resample, and the achieved significance level calculated as the number of permutations with ω2 values greater than or equal to the original two-sample ω2 divided by the total number of permutations.
Johnson et al. Genome Biology 2011 12:R21 doi:10.1186/gb-2011-12-3-r21