HLA Genotype Imputation with Attribute Bagging


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Documentation for package ‘HIBAG’ version 1.34.1

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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