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BIGDAWG (version 3.0.3)

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

391

Version

3.0.3

License

GPL (>= 3)

Issues

Pull Requests

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Repository

https://github.com/IgDAWG/BIGDAWG

Homepage

http://tools.immunogenomics.org/

Maintainer

Steven Mack

Last Published

November 17th, 2021

Functions in BIGDAWG (3.0.3)

AAtable.builder

Amino Acid Contingency Table Build

Amino Acid Wrapper

AlignObj.Create

Alignment Object Creator

AlignObj.Update

Updated Alignment Object Creator

Amino Acid Analysis Function

Check.Params.GLS

Check Input Parameters for GLS conversion

Check Data Structure

DRB345.Check.Zygosity

DRB345 haplotype zygosity checker single locus

Tabular Data Locus Format Tool

DRB345 Expected

Contingency Table Check

Function to Check Release Versions

Contingency Table Amino Acid ChiSq Testing

CheckString.Allele

GL String Allele Check

AlignmentFilter

Alignment Filter

CheckString.Locus

GL String Locus Check

Error Code Display and Logging

Locus Ordering for GL2Tab

Haplotype Analysis Function for Multicore

HLA P group Finder

Genotype List String to Tabular Data Conversion

MergeData_Output

Data Object Merge and Output

Filter Exon Specific Alignment Sections

Condensing Exon Specific Alignments to Single Dataframe

BIGDAWG Main Wrapper Function

Append Genetic System Locus Designation to Allele String

Build Output Matrix for GL2Tab Conversion

HLA Formatting Check for Amino Acid Analysis

Check Cores Parameters

HLA P group File Formatter

Creation of a 2x2 table using the indicated orientation.

Case Control Odds Ratio Calculation from Epicalc list variation

Case Control Odds Ratio Calculation from Epicalc

Create.Null.Table

Create Empty Table

DRB345 Column Processing

HLA Loci Legitimacy Check for Amino Acid Analysis

Expression Variant Suffix Removal

Genotype Combination Maker

DRB345.Check.Wrapper

DRB345 haplotype zygosity wrapper

Replace or Fill 00:00 allele strings

Chi square matrices

getAllele.Count

Recompute number of alleles

ExonPtnAlign.Create

Protein Exon Alignment Formatter

Check Input Parameters

Haplotype Wrapper for Multicore

Exon protein alignments.

Ambiguous Alleles Locus Name Formatting

Data Summary Function

Hardy-Weinbery Wrapper

Prepare imported data

Strict Chi-squared Contingency Table Test

Example HLA Dataset

Locus Analysis Function

Genotype List String Expander

Haplotype List Builder

Replace absent allele strings

Case-Control Odds ratio calculation and graphing

Genotype List String to Tabular Data Conversion

Genotype List String Conversion

HLA Allele Legitimacy Check for Amino Acid Analysis

HLA trimming function

Contextual Binning Chi-squared Contingency Table Test

Removes System and Locus from Alleles

Hardy Weinbergy Equilibrium Function

Hardy Weinbergy Equilibrium Function

Chi square test statistic

Genotype List String Condenser

Haplotype Name Builder

File Name Extraction

Locus Condenser for Tab2GL

Update function for protein aligment upon new IMGT HLA data release

Haplotype missing Allele summary function

Haplotype Table Maker

Observed Frequency