BG2

This is the development version of BG2; for the stable release version, see BG2.

Performs Bayesian GWAS analysis for non-Gaussian data using BG2

Bioconductor version: Development (3.21)

This package is built to perform GWAS analysis for non-Gaussian data using BG2. The BG2 method uses penalized quasi-likelihood along with nonlocal priors in a two step manner to identify SNPs in GWAS analysis. The research related to this package was supported in part by National Science Foundation awards DMS 1853549 and DMS 2054173.

Author: Jacob Williams [aut, cre] (ORCID: ), Shuangshuang Xu [aut], Marco Ferreira [aut] (ORCID: )

Maintainer: Jacob Williams <jwilliams at vt.edu>

Citation (from within R, enter citation("BG2")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BG2")

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("BG2")

BG2	HTML	R Script
Reference Manual	PDF
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AssayDomain, Bayesian, GenomeWideAssociation, SNP, Software
Version	1.7.0
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.2.0)
Imports	GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), MASS (>= 7.3-58.1), stats (>= 4.2.2)
System Requirements
URL

Suggests	BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 3.0.0)
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Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	BG2_1.7.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/BG2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BG2
Bioc Package Browser	https://code.bioconductor.org/browse/BG2/
Package Short Url	https://bioconductor.org/packages/BG2/
Package Downloads Report	Download Stats