Case-Control Analysis of Multi-Allelic Loci


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Documentation for package ‘BIGDAWG’ version 1.4.0

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A Amino Acid Analysis Function
AA.df.check Contingency Table Check
AAtable.builder Amino Acid Contingency Table Build
AlignmentFilter Alignment Filter
AlignObj.Create Alignment Object Creator
AlignObj.Update Updated Alignment Object Creator
BIGDAWG BIGDAWG wrapper function
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
CheckAlleles Allele presence check
CheckHLA HLA formatting check
CheckLoci Loci presence check
CheckRelease Function to Check Release Versions
DRB345.parser DRB345 Column Processing
DRB345.zygosity DRB345 haplotype zygosity checker
Err.Log Error Code Display and Logging
EVSremoval Expression Variant Suffix Removal
ExonPtnAlign.Create Protein Exon Alignment Formatter
ExonPtnList Exon 2 (class II) or 2/3 (class I) protein alignments.
getAllele.Count Recompute number of alleles
getCS.Mat Chi square matrices
getCS.stat Chi square test statistic
GetField HLA trimming function
GetFiles File Fetcher
getHap Haplotype Table Maker
getObsFreq Observed Frequency
H Haplotype Analysis Function
HLA_data Example HLA Dataset
HWE.ChiSq Hardy Weinbergy Equilibrium Function
HWE.wrapper Hardy Weinbergy Equilibrium Function
L Locus Analysis Function
make2x2 Creation of a 2x2 table using the indicated orientation.
makeComb Genotype Combination Maker
PgrpExtract HLA P group Finder
PgrpFormat HLA P group File Formatter
PreCheck Data summary function
rmABstrings Replace absent allele strings
RunChiSq Chi-squared Contingency Table Test
TableMaker Table Maker
UpdateRelease Update function for protein aligment upon new IMGT HLA data release