A                       Amino Acid Analysis Function
A.wrapper               Amino Acid Wrapper
AA.df.check             Contingency Table Check
AAtable.builder         Amino Acid Contingency Table Build
AlignObj.Create         Alignment Object Creator
AlignObj.Update         Updated Alignment Object Creator
AlignmentFilter         Alignment Filter
BIGDAWG                 BIGDAWG wrapper function
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
EVSremoval              Expression Variant Suffix Removal
Err.Log                 Error Code Display and Logging
ExonPtnAlign.Create     Protein Exon Alignment Formatter
ExonPtnList             Exon 2 (class II) or 2/3 (class I) protein
                        alignments.
GetField                HLA trimming function
GetFiles                File Fetcher
H                       Haplotype Analysis Function
H.wrapper               Haplotype Wrapper
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
PgrpExtract             HLA P group Finder
PgrpFormat              HLA P group File Formatter
PreCheck                Data summary function
RunChiSq                Chi-squared Contingency Table Test
TableMaker              Table Maker
UpdateRelease           Update function for protein aligment upon new
                        IMGT HLA data release
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
getHap                  Haplotype Table Maker
getObsFreq              Observed Frequency
make2x2                 Creation of a 2x2 table using the indicated
                        orientation.
makeComb                Genotype Combination Maker
rmABstrings             Replace absent allele strings
