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 |