UpdateRelease

Character vector of loci that should be used to create new alignment object (default = HLA-A,B,C,DRB1/3/4/5,DQA1,DQB1,DPA1,DPB1).

Loci

Logical specifiying if update should be forced.

Force

Logical specifying if the original alignment file be restored.

Restore

This updates the protein aligment used in checking HLA loci and alleles as well as in 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). 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. 'Analytical methods for disease association
    studies with immunogenetic data.' Methods Mol Biol. 2012;882:245-66.

UpdateRelease: Update function for protein aligment upon new IMGT HLA data release

Description

Usage

Arguments