H.MC.wrapper

Data frame of genotype calls for set being analyzed.

Tabsub

Character vector of unique loci being analyzed.

loci

Character vector of genos column names.

loci.ColNames

The genotype columns of the loci set being analyzed.

genos

Case/Control or Phenotype groupings.

Haplotype argument carryover from main BIGDAWG function

All.Pairwise

Data return carryover from main BIGDAWG function

Output

Summary display carryover from main BIGDAWG function

Verbose

Cores carryover from main BIGDAWG function

Cores

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.MC.wrapper: Haplotype Wrapper for Multicore

Description

Usage

Arguments