UpdateRelease

Character string or vector of loci that should be added to default loci (default = HLA-A,B,C,DRB1/3/4/5,DQA1,DQB1,DPA1,DPB1).

Add.Loci

Logical specifiying if update should be forced.

Force

Logical specifying if the original alignment file be restored.

Restore

Logical indicating if error reporting should be written to file.

Output

This updates the protein aligment used in checking HLA loci and alleles as well as in the amino acid analysis. Alignment must exist in database (ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/alignments/) or update will fail.

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>.

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

Description

Usage

Arguments