Locus

The column names of the loci being analyzed.

loci.ColNames

genos

Case/Control or Phenotype groupings.

Logical specify if strict rare cell binning should be used in ChiSq test.

Strict.Bin

Exon protein alignment filtered for locus.

ExonAlign

Number of cores to use for analysis.

Cores

This is the workhorse function for the amino acid 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>.

A: Amino Acid Analysis Function

Description

Usage

Arguments