HIBAG

DOI: 10.18129/B9.bioc.HIBAG    

HLA Genotype Imputation with Attribute Bagging

Bioconductor version: Release (3.6)

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 <zhengx at u.washington.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HIBAG")

Documentation

HTML	R Script	HIBAG vignette html
PDF		Reference Manual
Text		NEWS

Details

biocViews	Genetics, Software, StatisticalMethod
Version	1.14.0
In Bioconductor since	BioC 3.1 (R-3.2) (3 years)
License	GPL-3
Depends	R (>= 3.2.0)
Imports	methods
LinkingTo
Suggests	parallel, knitr, gdsfmt(>= 1.2.2), SNPRelate(>= 1.1.6), ggplot2
SystemRequirements
Enhances
URL	http://github.com/zhengxwen/HIBAG http://zhengxwen.github.io/HIBAG http://www.biostat.washington.edu/~bsweir/HIBAG/
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	HIBAG_1.14.0.tar.gz
Windows Binary	HIBAG_1.14.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	HIBAG_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HIBAG
Package Short Url	http://bioconductor.org/packages/HIBAG/
Package Downloads Report	Download Stats