HIBAG -- HLA Genotype Imputation with Attribute Bagging


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Documentation for package ‘HIBAG’ version 1.2.5

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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
hlaAllele A list of HLA types
hlaAlleleClass Class of HLA Type
hlaAlleleDigit Trim HLA alleles
hlaAlleleSubset Get a subset of HLA types
hlaAttrBagClass The class of HIBAG model
hlaAttrBagging Build a HIBAG model
hlaAttrBagObj The class of HIBAG object
hlaBED2Geno Convert from PLINK BED format
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
hlaErrMsg The last error message
hlaFlankingSNP SNP IDs in Flanking Region
hlaGDS2Geno Convert from SNP GDS format
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
hlaGenoSwitchStrand Allele switching
hlaHaplo2Geno Get a genotype object from a specified haplotype object
hlaHaploSubset Get a subset of haplotypes
hlaLociInfo HLA Locus Information
hlaMakeSNPGeno Make a SNP genotype object
hlaMakeSNPHaplo Make a SNP haplotype object
hlaModelFiles Load a model object from files
hlaModelFromObj Build a model from "hlaAttrBagObj"
hlaModelToObj Convert "hlaAttrBagClass" to "hlaAttrBagObj"
hlaOutOfBag Out-of-bag estimation of overall accuracy, per-allele sensitivity, etc
hlaParallelAttrBagging Build a HIBAG model via parallel computation
hlaPredMerge Merge prediction results from multiple HIBAG models
hlaPublish Finalize a HIBAG model
hlaReport Format a report
hlaResource Model Resource Information
hlaSampleAllele Get sample IDs from HLA types with a filter
hlaSNPGenoClass The class of SNP genotypes
hlaSNPHaploClass The class of SNP haplotypes
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 "hlaAttrBagClass" object
plot.hlaAttrBagObj Plot a "hlaAttrBagObj" object
predict.hlaAttrBagClass HIBAG model prediction (in parallel)
print.hlaAttrBagClass Summarize a "hlaAttrBagClass" object
print.hlaAttrBagObj Summarize a "hlaAttrBagObj" object
summary.hlaAlleleClass Summarize a "hlaAlleleClass" object
summary.hlaAttrBagClass Summarize a "hlaAttrBagClass" object
summary.hlaAttrBagObj Summarize a "hlaAttrBagObj" object
summary.hlaSNPGenoClass Summarize the genotypic dataset
summary.hlaSNPHaploClass Summarize the haplotypic dataset