HIBAG
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see HIBAG.
HLA Genotype Imputation with Attribute Bagging
Bioconductor version: 3.19
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>
citation("HIBAG")):
Installation
To install this package, start R (version "4.4") 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 algorithm implementation | HTML | R Script |
| HIBAG vignette html | HTML | R Script |
| HLA association vignette html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Genetics, Software, StatisticalMethod |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.2.0) |
| Imports | methods, RcppParallel |
| System Requirements | C++11, GNU make |
| URL | https://github.com/zhengxwen/HIBAG https://hibag.s3.amazonaws.com/index.html |
See More
| Suggests | parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, markdown, rmarkdown, Rsamtools |
| Linking To | RcppParallel (>= 5.0.0) |
| 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_1.40.0.tar.gz |
| Windows Binary (x86_64) | HIBAG_1.40.0.zip (64-bit only) |
| macOS Binary (x86_64) | HIBAG_1.40.0.tgz |
| macOS Binary (arm64) | HIBAG_1.40.0.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 |