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BIGDAWG (version 2.3)

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) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) . 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) .

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Version

Install

install.packages('BIGDAWG')

Monthly Downloads

454

Version

2.3

License

GPL (>= 3)

Issues

Pull Requests

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Repository

https://github.com/IgDAWG/BIGDAWG

Homepage

http://tools.immunogenomics.org/

Maintainer

Steve Mack

Last Published

November 12th, 2019

Functions in BIGDAWG (2.3)

HLA Allele Legitimacy Check for Amino Acid Analysis

CheckString.Allele

GL String Allele Check

Create.Null.Table

Create Empty Table

Genotype List String to Tabular Data Conversion

Check.Params.GLS

Check Input Parameters for GLS conversion

Hardy Weinbergy Equilibrium Function

DRB345.Check.Wrapper

DRB345 haplotype zygosity wrapper

Build Output Matrix for GL2Tab Conversion

Check Input Parameters

Genotype List String Conversion

HLA Formatting Check for Amino Acid Analysis

Check Cores Parameters

HLA Loci Legitimacy Check for Amino Acid Analysis

HLA trimming function

Locus Condenser for Tab2GL

Genotype List String Condenser

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

CheckString.Locus

GL String Locus Check

Replace or Fill 00:00 allele strings

Hardy-Weinbery Wrapper

Haplotype Table Maker

DRB345 Column Processing

Example HLA Dataset

Chi-squared Contingency Table Test

Case Control Odds Ratio Calculation from Epicalc

Function to Check Release Versions

DRB345 Expected

Observed Frequency

Case Control Odds Ratio Calculation from Epicalc list variation

Removes System and Locus from Alleles

Hardy Weinbergy Equilibrium Function

Haplotype Analysis Function for Multicore

Haplotype Wrapper for Multicore

DRB345.Check.Zygosity

DRB345 haplotype zygosity checker single locus

Check Data Structure

Expression Variant Suffix Removal

Error Code Display and Logging

Locus Ordering for GL2Tab

ExonPtnAlign.Create

Protein Exon Alignment Formatter

Genotype List String Expander

Data Summary Function

HLA P group File Formatter

Locus Analysis Function

Ambiguous Alleles Locus Name Formatting

Tabular Data Locus Format Tool

Update function for protein aligment upon new IMGT HLA data release

Case-Control Odds ratio calculation and graphing

Haplotype List Builder

Chi square matrices

getAllele.Count

Recompute number of alleles

MergeData_Output

Data Object Merge and Output

HLA P group Finder

Haplotype missing Allele summary function

Chi square test statistic

Genotype List String to Tabular Data Conversion

Prepare imported data

File Name Extraction

Replace absent allele strings

Genotype Combination Maker

Haplotype Name Builder

Creation of a 2x2 table using the indicated orientation.

BIGDAWG Main Wrapper Function

AlignmentFilter

Alignment Filter

Amino Acid Analysis Function

AlignObj.Create

Alignment Object Creator

Contingency Table Check

Append Genetic System Locus Designation to Allele String

AlignObj.Update

Updated Alignment Object Creator

Amino Acid Wrapper

AAtable.builder

Amino Acid Contingency Table Build