# Case-Control Analysis of Multi-Allelic Loci

## Documentation for package ‘BIGDAWG’ version 3.0.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
AlignmentFilter | Alignment Filter
AlignObj.Create | Alignment Object Creator
AlignObj.Update | Updated Alignment Object Creator
Append.System | Append Genetic System Locus Designation to Allele String
BIGDAWG | BIGDAWG Main Wrapper Function
Build.Matrix | Build Output Matrix for GL2Tab Conversion
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
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
Err.Log | Error Code Display and Logging
EVSremoval | Expression Variant Suffix Removal
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
getAllele.Count | Recompute number of alleles
getCS.Mat | Chi square matrices
getCS.stat | Chi square test statistic
GetField | HLA trimming function
getFileName | File Name Extraction
GetFiles | File Fetcher
getHap | Haplotype Table Maker
getObsFreq | Observed Frequency
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
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
L.wrapper | Locus Wrapper
make2x2 | Creation of a 2x2 table using the indicated orientation.
makeComb | Genotype Combination Maker
MergeData_Output | Data Object Merge and Output
PgrpExtract | HLA P group Finder
PgrpFormat | HLA P group File Formatter
PreCheck | Data Summary Function
prepData | Prepare imported data
rmABstrings | Replace absent allele strings
RunChiSq | Strict Chi-squared Contingency Table Test
RunChiSq_c | Contextual Binning Chi-squared Contingency Table Test
Stripper | Removes System and Locus from Alleles
summaryGeno.2 | Haplotype missing Allele summary function
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