HIBAG

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>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HIBAG")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HIBAG")

 

HTML	R Script	HIBAG algorithm implementation
HTML	R Script	HIBAG vignette html
HTML	R Script	HLA association vignette html
PDF		Reference Manual
Text		NEWS

Details

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
Enhances
URL	https://github.com/zhengxwen/HIBAG https://hibag.s3.amazonaws.com/index.html
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	HIBAG_1.36.4.tar.gz
Windows Binary	HIBAG_1.36.4.zip
macOS Binary (x86_64)	HIBAG_1.36.4.tgz
macOS Binary (arm64)	HIBAG_1.36.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HIBAG
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HIBAG
Bioc Package Browser	https://code.bioconductor.org/browse/HIBAG/
Package Short Url	https://bioconductor.org/packages/HIBAG/
Package Downloads Report	Download Stats