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 |