Man pages for pappasd/BIGDAWG
Case-Control Analysis of Multi-Allelic Loci
| 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 Main 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... |
| 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 |
| DRB345.parser | DRB345 Column Processing |
| 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 |
| HLA_data | Example HLA Dataset |
| HWE.ChiSq | Hardy Weinbergy Equilibrium Function |
| HWE.wrapper | Hardy-Weinbery Wrapper |
| 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... |
