buildHAPsets

Combination of loci to extraction from genos

Combn

The genotype columns of the loci set being analyzed.

genos

Character vector of unique loci being analyzed.

loci

Character vector of genos column names.

loci.ColNames

Builds table of haplotypes from combinations

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>.

buildHAPsets: Haplotype List Builder

Description

Usage

Arguments