A                       Amino Acid Analysis Function
A.wrapper               Amino Acid Wrapper
AA.df.check             Contingency Table Check
AA.df.cs                Contingency Table Amino Acid ChiSq Testing
AAtable.builder         Amino Acid Contingency Table Build
AlignObj.Create         Alignment Object Creator
AlignObj.Update         Updated Alignment Object Creator
AlignmentFilter         Alignment Filter
Append.System           Append Genetic System Locus Designation to
                        Allele String
BIGDAWG                 BIGDAWG Main Wrapper Function v1.1 Livia Tran
                        March 26, 2026
Build.Matrix            Build Output Matrix for GL2Tab Conversion
Check.Cores             Check Cores Parameters
Check.Data              Check Data Structure
Check.Params            Check Input Parameters
Check.Params.GLS        Check Input Parameters for GLS conversion
CheckAlleles            HLA Allele Legitimacy Check for Amino Acid
                        Analysis
CheckHLA                HLA Formatting Check for Amino Acid Analysis
CheckLoci               HLA Loci Legitimacy Check for Amino Acid
                        Analysis
CheckRelease            Function to Check Release Versions
CheckString.Allele      GL String Allele Check
CheckString.Locus       GL String Locus Check
Condense.EPL            Condensing Exon Specific Alignments to Single
                        Dataframe
Create.Null.Table       Create Empty Table
DRB345.Check.Wrapper    DRB345 haplotype zygosity wrapper
DRB345.Check.Zygosity   DRB345 haplotype zygosity checker single locus
DRB345.Exp              DRB345 Expected
DRB345.parser           DRB345 Column Processing
EVSremoval              Expression Variant Suffix Removal
Err.Log                 Error Code Display and Logging
Exon.Filter             Filter Exon Specific Alignment Sections
ExonPtnAlign.Create     Protein Exon Alignment Formatter
ExonPtnList             Exon protein alignments.
Filler                  Replace or Fill 00:00 allele strings
Format.Allele           Ambiguous Alleles Locus Name Formatting
Format.Tab              Tabular Data Locus Format Tool
GL2Tab.Loci             Locus Ordering for GL2Tab
GL2Tab.Sub              Genotype List String Expander
GL2Tab.wrapper          Genotype List String to Tabular Data Conversion
GLSconvert              Genotype List String Conversion
GetField                HLA trimming function
GetFiles                File Fetcher
H.MC                    Haplotype Analysis Function for Multicore
H.MC.wrapper            Haplotype Wrapper for Multicore
HLA_data                Example HLA Dataset
HWE                     Hardy Weinbergy Equilibrium Function
HWE.ChiSq               Hardy Weinbergy Equilibrium Function
HWE.wrapper             Hardy-Weinbery Wrapper
L                       Locus Analysis Function 25Jun2025
L.wrapper               Locus Wrapper
MergeData_Output        Data Object Merge and Output
PgrpExtract             HLA P group Finder
PgrpFormat              HLA P group File Formatter
PreCheck                Data Summary Function
RunChiSq                Strict Chi-squared Contingency Table Test
RunChiSq_c              Contextual Binning Chi-squared Contingency
                        Table Test
Stripper                Removes System and Locus from Alleles
Tab2GL.Loci             Locus Condenser for Tab2GL
Tab2GL.Sub              Genotype List String Condenser
Tab2GL.wrapper          Genotype List String to Tabular Data Conversion
TableMaker              Table Maker
UpdateRelease           Update function for protein aligment upon new
                        IMGT HLA data release
buildHAPnames           Haplotype Name Builder
buildHAPsets            Haplotype List Builder
cci                     Case-Control Odds ratio calculation and
                        graphing
cci.pval                Case Control Odds Ratio Calculation from
                        Epicalc
cci.pval.list           Case Control Odds Ratio Calculation from
                        Epicalc list variation
getAllele.Count         Recompute number of alleles
getCS.Mat               Chi square matrices
getCS.stat              Chi square test statistic
getFileName             File Name Extraction
getHap                  Haplotype Table Maker
getObsFreq              Observed Frequency
make2x2                 Creation of a 2x2 table using the indicated
                        orientation.
makeComb                Genotype Combination Maker
prepData                Prepare imported data v 1.1 10 December 2025
rmABstrings             Replace absent allele strings
summaryGeno.2           Haplotype missing Allele summary function
