Package 'BIGDAWG'

Title: Case-Cotrol 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) <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]
Maintainer: Steve Mack <[email protected]>
License: GPL (>= 3)
Version: 3.1.0
Built: 2026-09-27 18:41:45 UTC
Source: https://github.com/cranhaven/cranhaven.r-universe.dev

Help Index

Amino Acid Analysis Function

Description

This is the workhorse function for the amino acid analysis.

Usage

A(Locus, loci.ColNames, genos, grp, Strict.Bin, ExonAlign, Cores)

Arguments

Locus

Locus being analyzed.
loci.ColNames

The column names of the loci being analyzed.
genos

Genotype table.
grp

Case/Control or Phenotype groupings.
Strict.Bin

Logical specify if strict rare cell binning should be used in ChiSq test.
ExonAlign

Exon protein alignment filtered for locus.
Cores

Number of cores to use for analysis.

Note

This function is for internal BIGDAWG use only.

Amino Acid Wrapper

Description

Wrapper function for amino acid analysis.

Usage

A.wrapper(
  loci,
  loci.ColNames,
  genos,
  grp,
  Exon,
  EPL,
  Cores,
  Strict.Bin,
  Output,
  Verbose
)

Arguments

loci

Loci being analyzed.
loci.ColNames

The column names of the loci being analyzed.
genos

Genotype table.
grp

Case/Control or Phenotype groupings.
Exon

Exon(s)for targeted analysis.
EPL

Protein Alignment List.
Cores

Number of cores to use for analysis.
Strict.Bin

Logical specify if strict rare cell binning should be used in ChiSq test
Output

Data return carryover from main BIGDAWG function
Verbose

Summary display carryover from main BIGDAWG function

Note

This function is for internal BIGDAWG use only.

Contingency Table Check

Description

Checks amino acid contingency table data frame to ensure required variation exists.

Usage

AA.df.check(x, Strict.Bin)

Arguments

x

contingency table.
Strict.Bin

Logical specify if strict rare cell binning should be used in ChiSq test.

Note

This function is for internal BIGDAWG use only.

Contingency Table Amino Acid ChiSq Testing

Description

Runs ChiSq test on amino acid contingency table data frames.

Usage

AA.df.cs(x, Strict.Bin)

Arguments

x

contingency table.
Strict.Bin

Logical specify if strict rare cell binning should be used in ChiSq test.

Note

This function is for internal BIGDAWG use only.

Amino Acid Contingency Table Build

Description

Build Contingency Tables for Amino Acid Analysis.

Usage

AAtable.builder(x, y)

Arguments

x

Filtered alignmnet list element.
y

Phenotype groupings.

Note

This function is for internal BIGDAWG use only.

Alignment Filter

Description

Filter Protein Exon Alignment File for Specific Alleles.

Usage

AlignmentFilter(Align, Alleles, Locus)

Arguments

Align

Protein Alignment Object.
Alleles

to be pulled.
Locus

Locus to be filtered against.

Note

This function is for internal BIGDAWG use only.

Alignment Object Creator

Description

Create Object for Exon Protein Alignments.

Usage

AlignObj.Create(Loci, Release, RefTab)

Arguments

Loci

Loci to be bundled.
Release

IMGT/HLA database release version.
RefTab

Data of reference exons used for protein alignment creation.

Note

This function is for internal BIGDAWG use only.

Updated Alignment Object Creator

Description

Synthesize Object for Exon Protein Alignments.

Usage

AlignObj.Update(Loci, Release, RefTab)

Arguments

Loci

Loci to be bundled.
Release

IMGT/HLA database release version.
RefTab

Data of reference exons used for protein alignment creation.

Note

This function is for internal BIGDAWG use only.

Append Genetic System Locus Designation to Allele String

Description

Adds genetic system (HLA/KIR) to each allele name

Usage

Append.System(x, df.name)

Arguments

x

Vector Column genotypes to append
df.name

String SystemLocus name for each allele.

Note

This function is for internal use only.

BIGDAWG Main Wrapper Function v1.1 Livia Tran March 26, 2026

Description

This is the main wrapper function for each analysis.

Usage

BIGDAWG(
  Data,
  HLA = TRUE,
  Run.Tests,
  Loci.Set,
  Exon,
  All.Pairwise = FALSE,
  Trim = FALSE,
  Res = 2,
  EVS.rm = FALSE,
  Missing = 2,
  Strict.Bin = FALSE,
  Cores.Lim = 1L,
  Results.Dir,
  Return = FALSE,
  Output = TRUE,
  Merge.Output = FALSE,
  Verbose = TRUE,
  Data.Type = "Locus"
)

Arguments

Data

Name of the genotype data file.
HLA

Logical Indicating whether data is HLA class I/II genotyping data only.
Run.Tests

Specifics which tests to run.
Loci.Set

Input list defining which loci to use for analyses (combinations permitted).
Exon

Numeric Exon(s) for targeted amino acid analysis.
All.Pairwise

Logical indicating whether all pairwise loci should be analyzed in haplotype analysis.
Trim

Logical indicating if HLA alleles should be trimmed to a set resolution.
Res

Numeric setting what desired resolution to trim HLA alleles.
EVS.rm

Logical indicating if expression variant suffixes should be removed.
Missing

Numeric setting allowable missing data for running analysis (may use "ignore").
Strict.Bin

Logical specify if strict rare cell binning should be used in ChiSq test.
Cores.Lim

Integer setting the number of cores accessible to BIGDAWG (Windows limit is 1 core).
Results.Dir

Optional, string of full path directory name for BIGDAWG output.
Return

Logical Should analysis results be returned as list.
Output

Logical Should analysis results be written to output directory.
Merge.Output

Logical Should analysis results be merged into a single file for easy access.
Verbose

Logical Should a summary of each analysis be displayed in console.
Data.Type

String describing the data type in the provided dataset. The default is set to 'Locus'. Options are 'Locus' or 'Motif'.

Examples

## Not run: 
### The following examples use the synthetic data set bundled with BIGDAWG

# Haplotype analysis with no missing genotypes for two loci sets
# Significant haplotype association with phenotype
# BIGDAWG(Data="HLA_data", Run.Tests="H", Missing=0, Loci.Set=list(c("DRB1","DQB1")))

# Hardy-Weinberg and Locus analysis ignoring missing data
# Significant locus associations with phenotype at all but DQB1
# BIGDAWG(Data="HLA_data", Run.Tests="L", Missing="ignore")

# Hardy-Weinberg analysis trimming data to 2-Field resolution with no output to files (console only)
# Significant locus deviation at DQB1
BIGDAWG(Data="HLA_data", Run.Tests="HWE", Trim=TRUE, Res=2, Output=FALSE)

## End(Not run)

Build Output Matrix for GL2Tab Conversion

Description

Initializes output matrix format for GL2Tab conversion

Usage

Build.Matrix(System, Loci)

Arguments

System

Character Genetic system HLA- or KIR
Loci

The loci for header names

Note

This function is for internal use only.

Haplotype Name Builder

Description

Builds table of names for HAPsets

Usage

buildHAPnames(Combn, loci)

Arguments

Combn

Combination of loci to extraction from genos
loci

Character vector of unique loci being analyzed.

Note

This function is for internal BIGDAWG use only.

Haplotype List Builder

Description

Builds table of haplotypes from combinations

Usage

buildHAPsets(Combn, genos, loci, loci.ColNames)

Arguments

Combn

Combination of loci to extraction from genos
genos

The genotype columns of the loci set being analyzed.
loci

Character vector of unique loci being analyzed.
loci.ColNames

Character vector of genos column names.

Note

This function is for internal BIGDAWG use only.

Case-Control Odds ratio calculation and graphing

Description

cci function port epicalc version 2.15.1.0 (Virasakdi Chongsuvivatwong, 2012)

Usage

cci(
  caseexp,
  controlex,
  casenonex,
  controlnonex,
  cctable = NULL,
  graph = FALSE,
  design = "cohort",
  main,
  xlab,
  ylab,
  xaxis,
  yaxis,
  alpha = 0.05,
  fisher.or = TRUE,
  exact.ci.or = TRUE,
  decimal = 2
)

Arguments

caseexp

Number of cases exposed
controlex

Number of controls exposed
casenonex

Number of cases not exosed
controlnonex

Number of controls not exposed
cctable

A 2-by-2 table. If specified, will supercede the outcome and exposure variables
graph

If TRUE (default), produces an odds ratio plot
design

Specification for graph; can be "case control","case-control", "cohort" or "prospective"
main

main title of the graph
xlab

label on X axis
ylab

label on Y axis
xaxis

two categories of exposure in graph
yaxis

two categories of outcome in graph
alpha

level of significance
fisher.or

whether odds ratio should be computed by the exact method
exact.ci.or

whether confidence limit of the odds ratio should be computed by the exact method
decimal

number of decimal places displayed

Note

This function is for internal BIGDAWG use only.

Case Control Odds Ratio Calculation from Epicalc

Description

Calculates odds ratio and pvalues from 2x2 table

Usage

cci.pval(x)

Arguments

x

List of 2x2 matrices for calculation, output of TableMaker.

Note

This function is for internal BIGDAWG use only.

Case Control Odds Ratio Calculation from Epicalc list variation

Description

Variation of the cci.pval function

Usage

cci.pval.list(x)

Arguments

x

List of 2x2 matrices to apply the cci.pval function. List output of TableMaker.

Note

This function is for internal BIGDAWG use only.

Check Cores Parameters

Description

Check cores limitation for OS compatibility

Usage

Check.Cores(Cores.Lim, Output)

Arguments

Cores.Lim

Integer How many cores can be used.
Output

Logical Should analysis results be written to output directory.

Check Data Structure

Description

Check data structure for successful conversion.

Usage

Check.Data(Data, System, Convert)

Arguments

Data

String Type of output.
System

Character Genetic system HLA or KIR
Convert

String Direction for conversion.

Note

This function is for internal use only.

Check Input Parameters

Description

Check input parameters for invalid entries.

Usage

Check.Params(
  HLA,
  Loci.Set,
  Exon,
  All.Pairwise,
  Trim,
  Res,
  EVS.rm,
  Missing,
  Cores.Lim,
  Return,
  Output,
  Merge.Output,
  Verbose
)

Arguments

HLA

Logical indicating whether data is HLA class I/II genotyping data only.
Loci.Set

Input list defining which loci to use for analyses (combinations permitted).
Exon

Numeric Exon(s) for targeted amino acid analysis.
All.Pairwise

Logical indicating whether all pairwise loci should be analyzed in haplotype analysis.
Trim

Logical indicating if HLA alleles should be trimmed to a set resolution.
Res

Numeric setting what desired resolution to trim HLA alleles.
EVS.rm

Logical indicating if expression variant suffixes should be removed.
Missing

Numeric setting allowable missing data for running analysis (may use "ignore").
Cores.Lim

Integer setting the number of cores accessible to BIGDAWG (Windows limit is 1 core).
Return

Logical Should analysis results be returned as list.
Output

Logical Should analysis results be written to output directory.
Merge.Output

Logical Should analysis results be merged into a single file for easy access.
Verbose

Logical Should a summary of each analysis be displayed in console.

Note

This function is for internal use only.

Check Input Parameters for GLS conversion

Description

Check input parameters for invalid entries.

Usage

Check.Params.GLS(
  Convert,
  File.Output,
  System,
  HZY.Red,
  DRB345.Check,
  Cores.Lim
)

Arguments

Convert

String Direction for conversion.
File.Output

String Type of output.
System

String Genetic system (HLA or KIR) of the data being converted
HZY.Red

Logical Reduction of homozygote genotypes to single allele.
DRB345.Check

Logical Check DR haplotypes for consistency and flag unusual haplotypes.
Cores.Lim

Integer How many cores can be used.

Note

This function is for internal use only.

HLA Allele Legitimacy Check for Amino Acid Analysis

Description

Checks available alleles against data to ensure complete overlap.

Usage

CheckAlleles(x, y)

Arguments

x

Exon protein list alignment object.
y

Genotypes from data file

Note

This function is for internal BIGDAWG use only.

HLA Formatting Check for Amino Acid Analysis

Description

Checks data to see if HLA data is properly formatted .

Usage

CheckHLA(x)

Arguments

x

All columns of HLA genotyping data.

Note

This function is for internal BIGDAWG use only.

HLA Loci Legitimacy Check for Amino Acid Analysis

Description

Checks available loci against data to ensure complete overlap.

Usage

CheckLoci(x, y)

Arguments

x

Loci available in exon protein list alignment object.
y

Unique column names

Note

This function is for internal BIGDAWG use only.

Function to Check Release Versions

Description

This updates the protein aligment used in checking HLA loci and alleles as well as in the amino acid analysis.

Usage

CheckRelease(Package = T, Alignment = T, Output = F)

Arguments

Package

Logical to check for BIGDAWG package versions
Alignment

Logical to check the IMGT/HLA database version for the alignment bundled with BIGDAWG.
Output

Should any error be written to a file

Note

Requires active internet connection.

GL String Allele Check

Description

GL String check for allele ambiguity formatting

Usage

CheckString.Allele(x)

Arguments

x

GL String to check against

Note

This function is for internal use only.

GL String Locus Check

Description

Check GL string for loci appearing in multiple gene fields.

Usage

CheckString.Locus(x, Loci)

Arguments

x

GL String to check against
Loci

Loci to check

Note

This function is for internal use only.

Condensing Exon Specific Alignments to Single Dataframe

Description

Combines multiple Exon Specific Alignments into a single Alignment object

Usage

Condense.EPL(EPL.Exon)

Arguments

EPL.Exon

Exon-Locus Specific Amino Acid Alignment.

Note

This function is for internal BIGDAWG use only.

Create Empty Table

Description

Creates matrix of NA for no result tables.

Usage

Create.Null.Table(Locus, Names, nr)

Arguments

Locus

Locus being analyzed.
Names

Column names for final matrix.
nr

Number of rows.

Note

This function is for internal BIGDAWG use only.

DRB345 haplotype zygosity wrapper

Description

Checks DR haplotypes for correct zygosity and flags unanticipated haplotypes

Usage

DRB345.Check.Wrapper(Genotype, Loci.DR)

Arguments

Genotype

Row of data set data frame following DRB345 parsing
Loci.DR

DRBx Loci of interest to test for consistency

Note

This function is for internal use only.

DRB345 haplotype zygosity checker single locus

Description

Checks DR haplotypes for correct zygosity and flags unanticipated haplotypes for a single DRBx

Usage

DRB345.Check.Zygosity(Locus, Genotype)

Arguments

Locus

Locus of interest to test for consistency
Genotype

Row of data set data frame following DRB345 parsing

Note

This function is for internal use only.

DRB345 Expected

Description

Checks DRB1 Genotype and Returns Expected DR345 Loci

Usage

DRB345.Exp(DRB1.Genotype)

Arguments

DRB1.Genotype

DRB1 Subject Genotypes

Note

This function is for internal use only.

DRB345 Column Processing

Description

Separates DRB345 column pair into separate columns for each locus

Usage

DRB345.parser(Tab)

Arguments

Tab

Data frame of sampleIDs, phenotypes, and genotypes

Note

This function is for internal BIGDAWG use only.

Error Code Display and Logging

Description

Displays error codes attributable to data formatting and Locus/Allele naming. Writes to log file.

Usage

Err.Log(Output, x, y = NULL, z = NULL)

Arguments

Output

Logical indicating if Error logging should be written to a file.
x

Log Code.
y

Misc information relevant to error.
z

Misc information relevant to error.

Note

This function is for internal BIGDAWG use only.

Expression Variant Suffix Removal

Description

Removes expression variant suffixes from HLA alleles in the exon protein alignment object.

Usage

EVSremoval(Locus, EPList)

Arguments

Locus

Locus to be filtered against.
EPList

Exon Protein Alignment Object

Note

This function is for internal BIGDAWG use only.

Filter Exon Specific Alignment Sections

Description

Filters the ExonPtnAlign object by locus and exon.

Usage

Exon.Filter(Locus, Exon, EPL.Locus, RefExons, E.Ptn.Starts)

Arguments

Locus

Locus being analyzed.
Exon

Exon being analyzed.
EPL.Locus

ExonPtnAlign object filtered by Locus
RefExons

Reference Exon Table
E.Ptn.Starts

Exon Protein Overlay Map

Note

This function is for internal BIGDAWG use only.

Protein Exon Alignment Formatter

Description

Dynamically creates an alignmnet of Allele exons for Analysis.

Usage

ExonPtnAlign.Create(Locus, RefTab)

Arguments

Locus

Locus alignment to be formatted.
RefTab

Reference exon protein information for alignment formatting.

Note

This function is for internal BIGDAWG use only.

Exon protein alignments.

Description

Alignment object for use in the amino acid analysis.

Usage

ExonPtnList

Format

A list where each element is an alignment dataframe for a single locus.

Replace or Fill 00:00 allele strings

Description

Replaces or Fills absent allele strings.

Usage

Filler(x, Locus = NULL, Type)

Arguments

x

Genotype
Locus

Locus column to adjust.
Type

String specifying whether to pad ('Fill') or leave blank ('Remove') absent calls

Note

This function is for internal use only.

Ambiguous Alleles Locus Name Formatting

Description

Remove or Append Locus name from/to allele in an ambiguous allele string

Usage

Format.Allele(x, Type)

Arguments

x

Allele String
Type

String specifying whether to strip ('off') or append ('on') locus prefix

Note

This function is for internal use only.

Tabular Data Locus Format Tool

Description

Correctly orders the expanded GL string

Usage

Format.Tab(x, Order)

Arguments

x

Single row of converted GL string
Order

Single row data frame for mapping converted GL strings

Note

This function is for internal use only.

Recompute number of alleles

Description

Using Freq.Final, recompute number of alleles

Usage

getAllele.Count(x)

Arguments

x

Locus specific contingency matrix getCS.Mat output.

Note

This function is for internal BIGDAWG use only.

Chi square matrices

Description

Chi Square contingency matrix builder with rare cell binning

Usage

getCS.Mat(Locus, genos.sub, Allele.Freq, Allele.Combn)

Arguments

Locus

Locus of interest.
genos.sub

Genotypes for locus of interest.
Allele.Freq

Allele frequencies.
Allele.Combn

Allele combinations.

Note

This function is for internal BIGDAWG use only.

Chi square test statistic

Description

Calculate chi square test statistic

Usage

getCS.stat(Locus, Freq.Final)

Arguments

Locus

Locus of interest.
Freq.Final

Contingency Matrix getCS.Mat output.

Note

This function is for internal BIGDAWG use only.

HLA trimming function

Description

Trim a properly formatted HLA allele to desired number of fields.

Usage

GetField(x, Res)

Arguments

x

HLA allele.
Res

Resolution desired.

Note

This function is for internal BIGDAWG use only.

File Name Extraction

Description

Function to extract file path.

Usage

getFileName(x)

Arguments

x

File name.

Note

This function is for internal use only.

File Fetcher

Description

Download Protein Alignment and Accessory Files

Usage

GetFiles(Loci)

Arguments

Loci

HLA Loci to be fetched. Limited Loci available.

Note

This function is for internal BIGDAWG use only.

Haplotype Table Maker

Description

Builds table of haplotypes

Usage

getHap(SID, HaploEM)

Arguments

SID

Index number (i.e., row number) of sample ID from genotype matrix.
HaploEM

Haplotype output object from haplo.stat::haplo.em function.

Note

This function is for internal BIGDAWG use only.

Observed Frequency

Description

Get observed frequency of genotypes

Usage

getObsFreq(x, genos.locus)

Arguments

x

Single genotype.
genos.locus

Locus genotypes.

Note

This function is for internal BIGDAWG use only.

Locus Ordering for GL2Tab

Description

Orders Locus Calls

Usage

GL2Tab.Loci(Locus, Genotype, System)

Arguments

Locus

Locus to condense
Genotype

Row of loci to condense
System

Character Genetic system HLA or KIR

Note

This function is for internal use only.

Genotype List String Expander

Description

Expands GL string into a table of adjacent loci

Usage

GL2Tab.Sub(x, System)

Arguments

x

Character GL string to expand
System

Character Genetic system HLA or KIR

Note

This function is for internal use only.

Genotype List String to Tabular Data Conversion

Description

Expands GL strings to columns of adjacent locus pairs.

Usage

GL2Tab.wrapper(df, System, Strip.Prefix, Abs.Fill, Cores)

Arguments

df

Data frame containing GL strings
System

Character Genetic system HLA or KIR
Strip.Prefix

Logical Should System/Locus prefixes be stripped from table data.
Abs.Fill

Logical Should absent loci special designations be used.
Cores

Integer How many cores can be used

Note

This function is for internal use only

Genotype List String Conversion

Description

Main Workhorse wrapper for cross converting columnar table to GL string representaion.

Usage

GLSconvert(
  Data,
  Convert,
  File.Output = "txt",
  System = "HLA",
  HZY.Red = FALSE,
  DRB345.Check = FALSE,
  Strip.Prefix = TRUE,
  Abs.Fill = FALSE,
  Cores.Lim = 1L
)

Arguments

Data

String File name or R Data Frame.
Convert

String Direction for conversion.
File.Output

String Type of File.Output.
System

String Genetic system (HLA or KIR) of the data being converted
HZY.Red

Logical Reduction of homozygote genotypes to single allele.
DRB345.Check

Logical Check DR haplotypes for consistency and flag unusual haplotypes.
Strip.Prefix

Logical Should System/Locus prefixes be stripped from table data.
Abs.Fill

Logical Should absent loci special designations be used.
Cores.Lim

Integer How many cores can be used.

Haplotype Analysis Function for Multicore

Description

This is the workhorse function for the haplotype analysis.

Usage

H.MC(genos.sub, grp, Strict.Bin, Verbose)

Arguments

genos.sub

The genotype columns of the loci(locus) set being analyzed.
grp

Case/Control or Phenotype groupings.
Strict.Bin

Logical specify if strict rare cell binning should be used in ChiSq test
Verbose

Summary display carryover from main BIGDAWG function

Note

This function is for internal BIGDAWG use only.

Haplotype Wrapper for Multicore

Description

Wrapper for main H function

Usage

H.MC.wrapper(
  SID,
  Tabsub,
  loci,
  loci.ColNames,
  genos,
  grp,
  All.Pairwise,
  Strict.Bin,
  Output,
  Verbose,
  Cores
)

Arguments

SID

Character vector of subject IDs.
Tabsub

Data frame of genotype calls for set being analyzed.
loci

Character vector of unique loci being analyzed.
loci.ColNames

Character vector of genos column names.
genos

The genotype columns of the loci set being analyzed.
grp

Case/Control or Phenotype groupings.
All.Pairwise

Haplotype argument carryover from main BIGDAWG function
Strict.Bin

Logical specify if strict rare cell binning should be used in ChiSq test
Output

Data return carryover from main BIGDAWG function
Verbose

Summary display carryover from main BIGDAWG function
Cores

Cores carryover from main BIGDAWG function

Note

This function is for internal BIGDAWG use only.

Example HLA Dataset

Description

A synthetic dataset of HLA genotypes for using bigdawg.

Usage

HLA_data

Format

A data frame with 2000 rows and 14 variables

Hardy Weinbergy Equilibrium Function

Description

This is the main function for the HWE analysis.

Usage

HWE(Tab)

Arguments

Tab

data frame of genotype files post processing.

Note

This function is for internal BIGDAWG use only.

Hardy Weinbergy Equilibrium Function

Description

This is the workhorse function for each group analysis.

Usage

HWE.ChiSq(genos.sub, loci, nloci)

Arguments

genos.sub

data frame of genotype files post processing.
loci

list of loci.
nloci

number of loci in list

Note

This function is for internal BIGDAWG use only.

Hardy-Weinbery Wrapper

Description

Wrapper for main HWE function

Usage

HWE.wrapper(Tab, Output, Verbose)

Arguments

Tab

Data frame of genotype files post processing.
Output

Data return carryover from main BIGDAWG function
Verbose

Summary display carryover from main BIGDAWG function

Note

This function is for internal BIGDAWG use only.

Locus Analysis Function 25Jun2025

Description

This is the workhorse function for the locus level analysis.

Usage

L(loci.ColNames, Locus, genos, grp, Strict.Bin)

Arguments

loci.ColNames

The column names of the loci being analyzed.
Locus

Locus being analyzed.
genos

Genotype table
grp

Case/Control or Phenotype groupings.
Strict.Bin

Logical specify if strict rare cell binning should be used in ChiSq test

Note

This function is for internal BIGDAWG use only.

Locus Wrapper

Description

Wrapper for main L function

Usage

L.wrapper(nloci, loci, loci.ColNames, genos, grp, Strict.Bin, Output, Verbose)

Arguments

nloci

Number of loci being analyzed.
loci

Loci being analyzed.
loci.ColNames

The column names of the loci being analyzed.
genos

Genotype table
grp

Case/Control or Phenotype groupings.
Strict.Bin

Logical specify if strict rare cell binning should be used in ChiSq test
Output

Data return carryover from main BIGDAWG function
Verbose

Summary display carryover from main BIGDAWG function

Note

This function is for internal BIGDAWG use only.

Creation of a 2x2 table using the indicated orientation.

Description

make2x2 function port epicalc version 2.15.1.0 (Virasakdi Chongsuvivatwong, 2012)

Usage

make2x2(caseexp, controlex, casenonex, controlnonex)

Arguments

caseexp

Number of cases exposed
controlex

Number of controls exposed
casenonex

Number of cases not exosed
controlnonex

Number of controls not exposed

Note

This function is for internal BIGDAWG use only.

Genotype Combination Maker

Description

Make data frame of possible genotype combinations

Usage

makeComb(x)

Arguments

x

Number of alleles.

Note

This function is for internal BIGDAWG use only.

Data Object Merge and Output

Description

Whole data set table construction of per haplotype for odds ratio, confidence intervals, and pvalues

Usage

MergeData_Output(BD.out, Run, OutDir)

Arguments

BD.out

Output of analysis as list.
Run

Tests that are to be run as defined by Run.Tests.
OutDir

Output directory defined by Results.Dir or default.

Note

This function is for internal BIGDAWG use only.

HLA P group Finder

Description

Identify P group for a given allele if exists.

Usage

PgrpExtract(x, y)

Arguments

x

Allele of interest.
y

Formatted P groups.

Note

This function is for internal BIGDAWG use only.

HLA P group File Formatter

Description

Format the hla_nom_p.txt read table object for a specific locus.

Usage

PgrpFormat(x, Locus)

Arguments

x

P group object from read.table command.
Locus

Locus to be filtered on.

Note

This function is for internal BIGDAWG use only.

Data Summary Function

Description

Summary function for sample population within data file.

Usage

PreCheck(Tab, All.ColNames, rescall, HLA, Verbose, Output)

Arguments

Tab

Loci available in exon protein list alignment object.
All.ColNames

Column names from genotype data.
rescall

HLA resolution set for analysis.
HLA

HLA BIGDAWG argument passed to function
Verbose

Summary display carryover from BIGDAWG function.
Output

Data output carryover form BIGDAWG function

Note

This function is for internal BIGDAWG use only.

Prepare imported data v 1.1 10 December 2025

Description

Prepare imported data for processing, checks, and analysis.

Usage

prepData(Tab, data_type)

Arguments

Tab

Genotypes dataframe.
data_type

The type of data being processed. Options are 'Locus' or 'Motif'.'

Note

This function is for internal BIGDAWG use only.

Replace absent allele strings

Description

Replaces allowable absent allele strings with ^ symbol.

Usage

rmABstrings(df)

Arguments

df

Genotypes dataframe.

Note

This function is for internal BIGDAWG use only.

Strict Chi-squared Contingency Table Test

Description

Calculates chi-squared contingency table tests and bins all rare cells.

Usage

RunChiSq(x)

Arguments

x

Contingency table.

Note

This function is for internal BIGDAWG use only.

Contextual Binning Chi-squared Contingency Table Test

Description

Calculates chi-squared contingency table tests and bins rare cells at 20

Usage

RunChiSq_c(x)

Arguments

x

Contingency table.

Note

This function is for internal BIGDAWG use only.

Removes System and Locus from Alleles

Description

Removes the System and Locus designations for alleles calls in GL2Tab

Usage

Stripper(x)

Arguments

x

Allele

Note

This function is for internal use only.

Haplotype missing Allele summary function

Description

Summary function for identifying missing alleles in a matrix of genotypes.

Usage

summaryGeno.2(geno, miss.val = 0)

Arguments

geno

Matrix of genotypes.
miss.val

Vector of codes for allele missing values.

Note

This function is for internal BIGDAWG use only and is ported from haplo.stats.

Locus Condenser for Tab2GL

Description

Condenses alleles calls of a single locus string using "+"

Usage

Tab2GL.Loci(Locus, Genotype, System, HZY.Red)

Arguments

Locus

Locus to condense
Genotype

Row of loci to condense
System

Character Genetic system HLA or KIR
HZY.Red

Logical Should homozygote genotypes be a single allele for non-DRB345.

Note

This function is for internal use only.

Genotype List String Condenser

Description

Condenses column of loci into a GL string using "^"

Usage

Tab2GL.Sub(x, System, HZY.Red)

Arguments

x

Row of loci to condense
System

Character Genetic system HLA or KIR
HZY.Red

Logical Should homozygote genotypes be a single allele for non-DRB345.

Note

This function is for internal use only.

Genotype List String to Tabular Data Conversion

Description

Expands GL strings to columns of adjacent locus pairs.

Usage

Tab2GL.wrapper(df, System, HZY.Red, Abs.Fill, Cores)

Arguments

df

Data frame containing GL strings
System

Character Genetic system HLA or KIR
HZY.Red

Logical Should homozygote genotypes be a single allele for non-DRB345.
Abs.Fill

Logical Should absent loci special designations be used
Cores

Integer How many cores can be used.

Note

This function is for internal use only.

Table Maker

Description

Table construction of per haplotype for odds ratio, confidence intervals, and pvalues

Usage

TableMaker(x)

Arguments

x

Contingency table with binned rare cells.

Note

This function is for internal BIGDAWG use only.

Update function for protein aligment upon new IMGT HLA data release

Description

This updates the protein aligment used in checking HLA loci and alleles as well as in the amino acid analysis.

Usage

UpdateRelease(Force = F, Restore = F, Output = F)

Arguments

Force

Logical specifiying if update should be forced.
Restore

Logical specifying if the original alignment file be restored.
Output

Logical indicating if error reporting should be written to file.