The classical test for a m-by-2 table is Pearson's chi-square test which maximizes over all linear combinations of the allele frequencies. When only one or a few categories are associated this test has low power and alternatives such as Zmax
and the likelihood ratio statistic of Terwilliger should have more power. Zmax
and Zclump take the maximum over possibilities while Terwilligers approach takes the average over the possibilities. This program gives p-values for Pearson's chi-square, Zmax
and two score statistics (S1/m
) that correspond to Terwilligers approach of using the average. These methods can be used to compare haplotype frequencies between cases and controls. The web version assumes phase known genotypes and requires a m-by-2 table for input. The download version can also deal with phase unknown haplotypes. In that case it requires SNP genotypes as input and the empirical p-value is estimated by calling the software TAGSNPS
to derive haplotype counts in each simulation step.