The genotype columns of the loci(locus) set being analyzed.

genos.sub

Case/Control or Phenotype groupings.

This is the workhorse function for the haplotype analysis.

Data sets and functions for chi-squared Hardy-Weinberg and case-control
association tests of highly polymorphic genetic data [e.g., human leukocyte antigen
(HLA) data]. Performs association tests at multiple levels of polymorphism
(haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach
JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a
common class to account for sparse cells in tables as described by Hollenbach JA,
Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.

H: Haplotype Analysis Function

Description

Usage

Arguments