DOI: 10.18129/B9.bioc.HIBAG  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see HIBAG.

HLA Genotype Imputation with Attribute Bagging

Bioconductor version: 3.17

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.

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

Maintainer: Xiuwen Zheng <zhengx at u.washington.edu>

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HTML R Script HIBAG algorithm implementation
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biocViews Genetics, Software, StatisticalMethod
Version 1.36.4
In Bioconductor since BioC 3.1 (R-3.2) (8.5 years)
License GPL-3
Depends R (>= 3.2.0)
Imports methods, RcppParallel
LinkingTo RcppParallel (>= 5.0.0)
Suggests parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, markdown, rmarkdown, Rsamtools
SystemRequirements C++11, GNU make
URL https://github.com/zhengxwen/HIBAG https://hibag.s3.amazonaws.com/index.html
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Source Package HIBAG_1.36.4.tar.gz
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