Case-Control Analysis of Multi-Allelic Loci

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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