# HLA Genotype Imputation with Attribute Bagging

## Documentation for package ‘HIBAG’ version 1.30.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

HIBAG-package | HLA Genotype Imputation with Attribute Bagging
HapMap_CEU_Geno | SNP genotypes of a study simulated from HapMap CEU genotypic data
HIBAG | HLA Genotype Imputation with Attribute Bagging
hlaAASeqClass | Class of HLA Amino Acid Sequence Type
hlaAllele | A list of HLA/KIR types
hlaAlleleClass | Class of HLA/KIR Type
hlaAlleleDigit | Trim HLA alleles
hlaAlleleSubset | Get a subset of HLA/KIR types
hlaAlleleToVCF | Convert HLA alleles to VCF
hlaAssocTest | Statistical Association Tests
hlaAssocTest.hlaAASeqClass | Statistical Association Tests
hlaAssocTest.hlaAlleleClass | Statistical Association Tests
hlaAttrBagClass | The class of HIBAG model
hlaAttrBagging | Build a HIBAG model
hlaAttrBagObj | The class of HIBAG object
hlaBED2Geno | Convert from PLINK BED format
hlaCheckAllele | Check SNP alleles
hlaCheckSNPs | Check the SNP predictors in a HIBAG model
hlaClose | Dispose a model object
hlaCombineAllele | Combine two datasets of HLA types
hlaCombineModelObj | Combine two HIBAG models together
hlaCompareAllele | Evaluate prediction accuracies
hlaConvSequence | Conversion From HLA Alleles to Amino Acid Sequences
hlaDistance | Distance matrix of HLA alleles
hlaFlankingSNP | SNP IDs or SNP genotypes in Flanking Region
hlaGDS2Geno | Import genotypes from a GDS file
hlaGeno2PED | Convert to PLINK PED format
hlaGenoAFreq | Allele Frequency
hlaGenoCombine | Combine two genotypic data sets into one
hlaGenoLD | Composite Linkage Disequilibrium
hlaGenoMFreq | Minor Allele Frequency
hlaGenoMRate | Missing Rates Per SNP
hlaGenoMRate_Samp | Missing Rates Per Sample
hlaGenoSubset | Get a subset of genotypes
hlaGenoSubsetFlank | SNP IDs or SNP genotypes in Flanking Region
hlaGenoSwitchStrand | Allele flipping if needed
hlaLDMatrix | Composite Linkage Disequilibrium in a Region
hlaLociInfo | HLA/KIR Locus Information
hlaMakeSNPGeno | Make a SNP genotype object
hlaModelFiles | Load a model object from files
hlaModelFromObj | Conversion between the in-memory model and the object that can be saved in a file
hlaModelToObj | Conversion between the in-memory model and the object that can be saved in a file
hlaOutOfBag | Out-of-bag estimation of overall accuracy, per-allele sensitivity, etc
hlaParallelAttrBagging | Build a HIBAG model via parallel computation
hlaPredict | HIBAG model prediction (in parallel)
hlaPredMerge | Merge prediction results from multiple HIBAG models
hlaPublish | Finalize a HIBAG model
hlaReport | Format a report
hlaReportPlot | Format a report with figures
hlaSampleAllele | Get sample IDs from HLA types with a filter
hlaSetKernelTarget | Set the CPU target
hlaSNPGenoClass | The class of SNP genotypes
hlaSNPID | Get SNP IDs and positions
hlaSplitAllele | Divide the samples randomly
hlaSubModelObj | Get a subset of individual classifiers
hlaUniqueAllele | Get unique HLA alleles
HLA_Type_Table | Four-digit HLA types of a study simulated from HapMap CEU
plot.hlaAttrBagClass | Plot a HIBAG model
plot.hlaAttrBagObj | Plot a HIBAG model
predict.hlaAttrBagClass | HIBAG model prediction (in parallel)
print.hlaAlleleClass | Summarize a "hlaAlleleClass" or "hlaAASeqClass" object
print.hlaAttrBagClass | Summarize a "hlaAttrBagClass" or "hlaAttrBagObj" object.
print.hlaAttrBagObj | Summarize a "hlaAttrBagClass" or "hlaAttrBagObj" object.
print.hlaSNPGenoClass | Summarize a SNP dataset
summary.hlaAASeqClass | Summarize a "hlaAlleleClass" or "hlaAASeqClass" object
summary.hlaAlleleClass | Summarize a "hlaAlleleClass" or "hlaAASeqClass" object
summary.hlaAttrBagClass | Summarize a "hlaAttrBagClass" or "hlaAttrBagObj" object.
summary.hlaAttrBagObj | Summarize a "hlaAttrBagClass" or "hlaAttrBagObj" object.
summary.hlaSNPGenoClass | Summarize a SNP dataset