Case-Control Analysis of Multi-Allelic Loci

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Documentation for package ‘BIGDAWG’ version 3.0.3

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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