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BIGDAWG (version 1.1.1)

Case-Control Analysis of Multi-Allelic Loci

Description

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.

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Version

Install

install.packages('BIGDAWG')

Monthly Downloads

247

Version

1.1.1

License

GPL (>= 3)

Maintainer

Steve Mack

Last Published

October 30th, 2015

Functions in BIGDAWG (1.1.1)

HLA formatting check

Example HLA Dataset

Exon 2 (class II) or 2/3 (class I) protein alignments.

Replace absent allele strings

Locus Analysis Function

HLA P group File Formatter

Data summary function

AlignObj.Update

Updated Alignment Object Creator

HLA trimming function

Chi square matrices

HLA P group Finder

Hardy Weinbergy Equilibrium Function

Case Control Odds Ratio Calculation from Epicalc

Genotype Combination Maker

Case Control Odds Ratio Calculation from Epicalc list variation

Case-Control Odds ratio calculation and graphing

BIGDAWG wrapper function

Creation of a 2x2 table using the indicated orientation.

Observed Frequency

ExonPtnAlign.Create

Protein Exon Alignment Formatter

Haplotype Analysis Function

Amino Acid Analysis Function

Update function for protein aligment upon new IMGT HLA data release

Allele presence check

Chi-squared Contingency Table Test

Expression Variant Suffix Removal

AAtable.builder

Amino Acid Contingency Table Build

Loci presence check

Contingency Table Check

AlignObj.Create

Alignment Object Creator

AlignmentFilter

Alignment Filter