Package: HIBAG 1.49.0

Xiuwen Zheng

HIBAG: HLA Genotype Imputation with Attribute Bagging

Imputes HLA classical alleles using GWAS SNP data, and it relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.

Authors:Xiuwen Zheng [aut, cre, cph], Bruce Weir [ctb, ths]

HIBAG_1.49.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HIBAG/json (API)

# Install 'HIBAG' in R:
install.packages('HIBAG', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zhengxwen/hibag/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • HapMap_CEU_Geno - SNP genotypes of a study simulated from HapMap CEU genotypic data
  • HLA_Type_Table - Four-digit HLA types of a study simulated from HapMap CEU

On BioConductor:HIBAG-1.49.0(bioc 3.24)HIBAG-1.48.0(bioc 3.23)

geneticsstatisticalmethodbioinformaticsgpuhlaimputationmhcsnpcpp

8.01 score 31 stars 55 scripts 548 downloads 22 mentions 60 exports 1 dependencies

Last updated from:ea64e9b835. Checks:1 WARNING, 11 NOTE, 1 OK, 1 FAIL. Indexed: yes.

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linux-devel-x86_64NOTE175
source / vignettesOK283
linux-release-arm64NOTE177
linux-release-x86_64NOTE200
macos-release-arm64NOTE156
macos-release-x86_64NOTE301
macos-oldrel-arm64NOTE158
macos-oldrel-x86_64NOTE370
windows-develNOTE194
windows-releaseNOTE200
windows-oldrelNOTE181
wasm-releaseFAIL124

Exports:hlaAllelehlaAlleleDigithlaAlleleSubsethlaAlleleToVCFhlaAssocTesthlaAssocTest.hlaAASeqClasshlaAssocTest.hlaAlleleClasshlaAttrBagginghlaBED2GenohlaCheckAllelehlaCheckSNPshlaClosehlaCombineAllelehlaCombineModelObjhlaCompareAllelehlaConvSequencehlaDistancehlaFlankingSNPhlaGDS2GenohlaGeno2PEDhlaGenoAFreqhlaGenoCombinehlaGenoLDhlaGenoMFreqhlaGenoMRatehlaGenoMRate_SamphlaGenoSubsethlaGenoSubsetFlankhlaGenoSwitchStrandhlaLDMatrixhlaLociInfohlaMakeSNPGenohlaModelFileshlaModelFromObjhlaModelToObjhlaOutOfBaghlaParallelAttrBagginghlaPredicthlaPredMergehlaPublishhlaReporthlaReportPlothlaSampleAllelehlaSetKernelTargethlaSNPIDhlaSplitAllelehlaSubModelObjhlaUniqueAlleleplot.hlaAttrBagClassplot.hlaAttrBagObjpredict.hlaAttrBagClassprint.hlaAlleleClassprint.hlaAttrBagClassprint.hlaAttrBagObjprint.hlaSNPGenoClasssummary.hlaAASeqClasssummary.hlaAlleleClasssummary.hlaAttrBagClasssummary.hlaAttrBagObjsummary.hlaSNPGenoClass

Dependencies:RcppParallel

New Implementation of the HIBAG Algorithm with Latest Intel Intrinsics
Benchmarks on building the training models | 1) Speedup factor using small training sets | 2) Speedup factor using medium training sets | 3) Speedup factor using large training sets | Multithreading | Session Info | References
Rendered fromImplementation.Rmdusingknitr::rmarkdown

Last update: 2022-07-16
Started: 2020-10-09

HIBAG -- an R Package for HLA Genotype Imputation with Attribute Bagging
Overview | Features | Examples | Pre-fit HIBAG Models for HLA Imputation | Build a HIBAG Model for HLA Genotype Imputation | Build and Predict in Parallel | Evaluate Overall Accuracy, Sensitivity, Specificity, etc | Evaluation in Figures | Report in Text | Report in Markdown | Report in LaTeX | Release HIBAG Models without Confidential Information | Release a Collection of HIBAG Models | Resources | Session Info | References
Rendered fromHIBAG.Rmdusingknitr::rmarkdown

Last update: 2022-07-16
Started: 2019-10-14

HIBAG -- an R Package for HLA Genotype Imputation with Attribute Bagging
Overview | Association Tests | Allelic Association | Amino Acid Association | Resources | Session Info | References
Rendered fromHLA_Association.Rmdusingknitr::rmarkdown

Last update: 2022-07-16
Started: 2020-09-24

Readme and manuals

Help Manual

Help pageTopics
HLA Genotype Imputation with Attribute BaggingHIBAG-package HIBAG
SNP genotypes of a study simulated from HapMap CEU genotypic dataHapMap_CEU_Geno
Four-digit HLA types of a study simulated from HapMap CEUHLA_Type_Table
Class of HLA Amino Acid Sequence TypehlaAASeqClass
A list of HLA/KIR typeshlaAllele
Class of HLA/KIR TypehlaAlleleClass
Trim HLA alleleshlaAlleleDigit
Get a subset of HLA/KIR typeshlaAlleleSubset
Convert HLA alleles to VCFhlaAlleleToVCF
Statistical Association TestshlaAssocTest hlaAssocTest.hlaAASeqClass hlaAssocTest.hlaAlleleClass
The class of HIBAG modelhlaAttrBagClass
Build a HIBAG modelhlaAttrBagging
The class of HIBAG objecthlaAttrBagObj
Convert from PLINK BED formathlaBED2Geno
Check SNP alleleshlaCheckAllele
Check the SNP predictors in a HIBAG modelhlaCheckSNPs
Dispose a model objecthlaClose
Combine two datasets of HLA typeshlaCombineAllele
Combine two HIBAG models togetherhlaCombineModelObj
Evaluate prediction accuracieshlaCompareAllele
Conversion From HLA Alleles to Amino Acid SequenceshlaConvSequence
Distance matrix of HLA alleleshlaDistance
SNP IDs or SNP genotypes in Flanking RegionhlaFlankingSNP hlaGenoSubsetFlank
Import genotypes from a GDS filehlaGDS2Geno
Convert to PLINK PED formathlaGeno2PED
Allele FrequencyhlaGenoAFreq
Combine two genotypic data sets into onehlaGenoCombine
Composite Linkage DisequilibriumhlaGenoLD
Minor Allele FrequencyhlaGenoMFreq
Missing Rates Per SNPhlaGenoMRate
Missing Rates Per SamplehlaGenoMRate_Samp
Get a subset of genotypeshlaGenoSubset
Allele flipping if neededhlaGenoSwitchStrand
Composite Linkage Disequilibrium in a RegionhlaLDMatrix
HLA/KIR Locus InformationhlaLociInfo
Make a SNP genotype objecthlaMakeSNPGeno
Load a model object from fileshlaModelFiles
Conversion between the in-memory model and the object that can be saved in a filehlaModelFromObj hlaModelToObj
Out-of-bag estimation of overall accuracy, per-allele sensitivity, etchlaOutOfBag
Build a HIBAG model via parallel computationhlaParallelAttrBagging
HIBAG model prediction (in parallel)hlaPredict predict.hlaAttrBagClass
Merge prediction results from multiple HIBAG modelshlaPredMerge
Finalize a HIBAG modelhlaPublish
Format a reporthlaReport
Format a report with figureshlaReportPlot
Get sample IDs from HLA types with a filterhlaSampleAllele
Set the CPU targethlaSetKernelTarget
The class of SNP genotypeshlaSNPGenoClass
Get SNP IDs and positionshlaSNPID
Divide the samples randomlyhlaSplitAllele
Get a subset of individual classifiershlaSubModelObj
Get unique HLA alleleshlaUniqueAllele
Plot a HIBAG modelplot.hlaAttrBagClass plot.hlaAttrBagObj
Summarize a ``hlaAttrBagClass'' or ``hlaAttrBagObj'' object.print.hlaAttrBagClass print.hlaAttrBagObj summary.hlaAttrBagClass summary.hlaAttrBagObj
Summarize a ``hlaAlleleClass'' or ``hlaAASeqClass'' objectprint.hlaAlleleClass summary.hlaAASeqClass summary.hlaAlleleClass
Summarize a SNP datasetprint.hlaSNPGenoClass summary.hlaSNPGenoClass