This package is no longer supported. The majority of the functionality
for conditional haplotype tests in population-based samples has been
implemented in PLINK, with a better interface
and more robust, faster computation: please use that from now on.
whap provides a method for testing SNP haplotype associations
with qualitative and quantitative traits in samples of
individuals with or without parental genotype data.
You are advised to look at the examples
first, then read all the instructions and follow
the more advanced tutorial, and
especially the warnings in
order to avoid common problems.
What whap can do
Analyse quantitative and qualitative traits
Handle unrelated individuals and/or parent-offspring trio data
Perform a regression-based haplotype association test for SNP data
Perform a secondary test based on pairwise haplotype similarity
Phase genotype data using a standard E-M approach, and handle
ambiguity in E-M inferred haplotypes
Include covariates and moderator variables
Flexibly constrain effects across haplotypes to tested nested models
Perform a robust within-family test when parental genotypes are present