Man pages for HIBAG
HLA Genotype Imputation with Attribute Bagging

HapMap_CEU_GenoSNP genotypes of a study simulated from HapMap CEU genotypic...
HIBAG-packageHLA Genotype Imputation with Attribute Bagging
hlaAASeqClassClass of HLA Amino Acid Sequence Type
hlaAlleleA list of HLA/KIR types
hlaAlleleClassClass of HLA/KIR Type
hlaAlleleDigitTrim HLA alleles
hlaAlleleSubsetGet a subset of HLA/KIR types
hlaAssocTestStatistical Association Tests
hlaAttrBagClassThe class of HIBAG model
hlaAttrBaggingBuild a HIBAG model
hlaAttrBagObjThe class of HIBAG object
hlaBED2GenoConvert from PLINK BED format
hlaCheckAlleleCheck SNP alleles
hlaCheckSNPsCheck the SNP predictors in a HIBAG model
hlaCloseDispose a model object
hlaCombineAlleleCombine two datasets of HLA types
hlaCombineModelObjCombine two HIBAG models together
hlaCompareAlleleEvaluate prediction accuracies
hlaConvSequenceConversion From HLA Alleles to Amino Acid Sequences
hlaDistanceDistance matrix of HLA alleles
hlaFlankingSNPSNP IDs or SNP genotypes in Flanking Region
hlaGDS2GenoConvert from SNP GDS format
hlaGeno2PEDConvert to PLINK PED format
hlaGenoAFreqAllele Frequency
hlaGenoCombineCombine two genotypic data sets into one
hlaGenoLDComposite Linkage Disequilibrium
hlaGenoMFreqMinor Allele Frequency
hlaGenoMRateMissing Rates Per SNP
hlaGenoMRate_SampMissing Rates Per Sample
hlaGenoSubsetGet a subset of genotypes
hlaGenoSwitchStrandAllele switching
hlaLDMatrixComposite Linkage Disequilibrium in a Region
hlaLociInfoHLA/KIR Locus Information
hlaMakeSNPGenoMake a SNP genotype object
hlaModelFilesLoad a model object from files
hlaModelFromObjConversion between the in-memory model and the object that...
hlaOutOfBagOut-of-bag estimation of overall accuracy, per-allele...
hlaParallelAttrBaggingBuild a HIBAG model via parallel computation
hlaPredictHIBAG model prediction (in parallel)
hlaPredMergeMerge prediction results from multiple HIBAG models
hlaPublishFinalize a HIBAG model
hlaReportFormat a report
hlaReportPlotFormat a report with figures
hlaSampleAlleleGet sample IDs from HLA types with a filter
hlaSetKernelTargetSet the CPU target
hlaSNPGenoClassThe class of SNP genotypes
hlaSNPIDGet SNP IDs and positions
hlaSplitAlleleDivide the samples randomly
hlaSubModelObjGet a subset of individual classifiers
HLA_Type_TableFour-digit HLA types of a study simulated from HapMap CEU
hlaUniqueAlleleGet unique HLA alleles
plot.hlaAttrBagObjPlot a HIBAG model
print.hlaAttrBagClassSummarize a "hlaAttrBagClass" or "hlaAttrBagObj" object.
summary.hlaAlleleClassSummarize a "hlaAlleleClass" or "hlaAASeqClass" object
summary.hlaSNPGenoClassSummarize a SNP dataset
HIBAG documentation built on March 24, 2021, 6 p.m.