Package: BIGDAWG 3.1.0

Steve Mack

BIGDAWG: Case-Cotrol Analysis of Multi-Allelic Loci

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>.

Authors:Derek Pappas [aut], Livia Tran [aut], Steve Mack [aut, cre], Jill Hollenbach [aut]

BIGDAWG_3.1.0.tar.gz
BIGDAWG_3.1.0.zip(r-4.7-any)BIGDAWG_3.1.0.zip(r-4.6-any)BIGDAWG_3.1.0.zip(r-4.5-any)
BIGDAWG_3.1.0.tgz(r-4.6-any)BIGDAWG_3.1.0.tgz(r-4.5-any)
BIGDAWG_3.1.0.tar.gz(r-4.7-any)BIGDAWG_3.1.0.tar.gz(r-4.6-any)
BIGDAWG_3.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BIGDAWG/json (API)

# Install 'BIGDAWG' in R:
install.packages('BIGDAWG', repos = c('https://cranhaven.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/igdawg/bigdawg/issues

On CRAN:

Conda:

archivedpackagesr-universe

4.32 score 5 stars 1 packages 621 downloads 7 mentions 77 exports 10 dependencies

Last updated from:16718317b2 (on package/BIGDAWG). Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develOK164
source / vignettesOK234
linux-releaseOK136
macos-releaseOK113
macos-oldrelOK149
windows-develOK122
windows-releaseOK95
windows-oldrelOK84
wasm-releaseOK129

Exports:AA.wrapperAA.df.checkAA.df.csAAtable.builderAlignmentFilterAlignObj.CreateAlignObj.UpdateAppend.SystemBIGDAWGBuild.MatrixbuildHAPnamesbuildHAPsetsccicci.pvalcci.pval.listCheck.CoresCheck.DataCheck.ParamsCheck.Params.GLSCheckAllelesCheckHLACheckLociCheckReleaseCheckString.AlleleCheckString.LocusCondense.EPLCreate.Null.TableDRB345.Check.WrapperDRB345.Check.ZygosityDRB345.ExpDRB345.parserErr.LogEVSremovalExon.FilterExonPtnAlign.CreateExonPtnListFillerFormat.AlleleFormat.TabgetAllele.CountgetCS.MatgetCS.statGetFieldgetFileNameGetFilesgetHapgetObsFreqGL2Tab.LociGL2Tab.SubGL2Tab.wrapperGLSconvertH.MCH.MC.wrapperHLA_dataHWEHWE.ChiSqHWE.wrapperLL.wrappermake2x2makeCombMergeData_OutputPgrpExtractPgrpFormatPreCheckprepDatarmABstringsRunChiSqRunChiSq_cStrippersummaryGeno.2Tab2GL.LociTab2GL.SubTab2GL.wrapperTableMakerUpdateRelease

Dependencies:arsenalevaluategluehaplo.statshighrknitrMASSxfunXMLyaml

BIGDAWG
Overview | Input Data | Data Output | Error Messages and Codes | Known Issues | Parameters | Examples | Updating the bundled IMGT/HLA protein alignment | Updating BIGDAWG to latest developmental versions
Rendered fromBIGDAWG.Rmdusingknitr::rmarkdown

Last update: 2026-09-27
Started: 2026-09-27

GLSconvert
Overview | Anatomy of a GL String | Input Data | Data Output | Parameters | Examples
Rendered fromGLSconvert.Rmdusingknitr::rmarkdown

Last update: 2026-09-27
Started: 2026-09-27

Readme and manuals

Help Manual

Help pageTopics
Amino Acid Analysis FunctionA
Amino Acid WrapperA.wrapper
Contingency Table CheckAA.df.check
Contingency Table Amino Acid ChiSq TestingAA.df.cs
Amino Acid Contingency Table BuildAAtable.builder
Alignment FilterAlignmentFilter
Alignment Object CreatorAlignObj.Create
Updated Alignment Object CreatorAlignObj.Update
Append Genetic System Locus Designation to Allele StringAppend.System
BIGDAWG Main Wrapper Function v1.1 Livia Tran March 26, 2026BIGDAWG
Build Output Matrix for GL2Tab ConversionBuild.Matrix
Haplotype Name BuilderbuildHAPnames
Haplotype List BuilderbuildHAPsets
Case-Control Odds ratio calculation and graphingcci
Case Control Odds Ratio Calculation from Epicalccci.pval
Case Control Odds Ratio Calculation from Epicalc list variationcci.pval.list
Check Cores ParametersCheck.Cores
Check Data StructureCheck.Data
Check Input ParametersCheck.Params
Check Input Parameters for GLS conversionCheck.Params.GLS
HLA Allele Legitimacy Check for Amino Acid AnalysisCheckAlleles
HLA Formatting Check for Amino Acid AnalysisCheckHLA
HLA Loci Legitimacy Check for Amino Acid AnalysisCheckLoci
Function to Check Release VersionsCheckRelease
GL String Allele CheckCheckString.Allele
GL String Locus CheckCheckString.Locus
Condensing Exon Specific Alignments to Single DataframeCondense.EPL
Create Empty TableCreate.Null.Table
DRB345 haplotype zygosity wrapperDRB345.Check.Wrapper
DRB345 haplotype zygosity checker single locusDRB345.Check.Zygosity
DRB345 ExpectedDRB345.Exp
DRB345 Column ProcessingDRB345.parser
Error Code Display and LoggingErr.Log
Expression Variant Suffix RemovalEVSremoval
Filter Exon Specific Alignment SectionsExon.Filter
Protein Exon Alignment FormatterExonPtnAlign.Create
Exon protein alignments.ExonPtnList
Replace or Fill 00:00 allele stringsFiller
Ambiguous Alleles Locus Name FormattingFormat.Allele
Tabular Data Locus Format ToolFormat.Tab
Recompute number of allelesgetAllele.Count
Chi square matricesgetCS.Mat
Chi square test statisticgetCS.stat
HLA trimming functionGetField
File Name ExtractiongetFileName
File FetcherGetFiles
Haplotype Table MakergetHap
Observed FrequencygetObsFreq
Locus Ordering for GL2TabGL2Tab.Loci
Genotype List String ExpanderGL2Tab.Sub
Genotype List String to Tabular Data ConversionGL2Tab.wrapper
Genotype List String ConversionGLSconvert
Haplotype Analysis Function for MulticoreH.MC
Haplotype Wrapper for MulticoreH.MC.wrapper
Example HLA DatasetHLA_data
Hardy Weinbergy Equilibrium FunctionHWE
Hardy Weinbergy Equilibrium FunctionHWE.ChiSq
Hardy-Weinbery WrapperHWE.wrapper
Locus Analysis Function 25Jun2025L
Locus WrapperL.wrapper
Creation of a 2x2 table using the indicated orientation.make2x2
Genotype Combination MakermakeComb
Data Object Merge and OutputMergeData_Output
HLA P group FinderPgrpExtract
HLA P group File FormatterPgrpFormat
Data Summary FunctionPreCheck
Prepare imported data v 1.1 10 December 2025prepData
Replace absent allele stringsrmABstrings
Strict Chi-squared Contingency Table TestRunChiSq
Contextual Binning Chi-squared Contingency Table TestRunChiSq_c
Removes System and Locus from AllelesStripper
Haplotype missing Allele summary functionsummaryGeno.2
Locus Condenser for Tab2GLTab2GL.Loci
Genotype List String CondenserTab2GL.Sub
Genotype List String to Tabular Data ConversionTab2GL.wrapper
Table MakerTableMaker
Update function for protein aligment upon new IMGT HLA data releaseUpdateRelease