HIBAG

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see HIBAG.

HLA Genotype Imputation with Attribute Bagging


Bioconductor version: 3.9

It is a software package for imputing HLA types using SNP data, and 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 <zhengxwen at gmail.com>

Citation (from within R, enter citation("HIBAG")):

Installation

To install this package, start R (version "3.6") 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")
HIBAG vignette html HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Genetics, Software, StatisticalMethod
Version 1.20.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL-3
Depends R (>= 3.2.0)
Imports methods
System Requirements
URL http://github.com/zhengxwen/HIBAG http://zhengxwen.github.io/HIBAG http://www.biostat.washington.edu/~bsweir/HIBAG/
See More
Suggests parallel, knitr, gdsfmt(>= 1.2.2), SNPRelate(>= 1.1.6), ggplot2, reshape2
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package HIBAG_1.20.0.tar.gz
Windows Binary HIBAG_1.20.0.zip
Mac OS X 10.11 (El Capitan) HIBAG_1.20.0.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
Old Source Packages for BioC 3.9 Source Archive