Haploview currently supports several types of association tests with a number of features:
- single SNP TDT and case/control tests
- block-based haplotype association tests
- user specified haplotype tests
- permutation significance testing
The following screenshots show some of these features for the dataset we've loaded. More information is available in the documentation.
Experiment-wide p-values can be generated by permutation, using the permutation tests tab. Here we show the results of 500 permutations on all the single SNPs and haplotype alleles in blocks for this dataset: