BG2
This is the released version of BG2; for the devel version, see BG2.
Performs Bayesian GWAS analysis for non-Gaussian data using BG2
DOI: 10.18129/B9.bioc.BG2
Bioconductor version: Release (3.23)
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]
, Shuangshuang Xu [aut], Marco Ferreira [aut]
Maintainer: Jacob Williams <jwilliams at vt.edu>
citation("BG2")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| LICENSE | Text |
Details
| biocViews | AssayDomain, Bayesian, GenomeWideAssociation, SNP, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 3.0.0) |
| 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 | BG2_1.12.0.tar.gz |
| Windows Binary (x86_64) | BG2_1.12.0.zip |
| macOS Binary (big-sur-x86_64) | BG2_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | BG2_1.12.0.tgz |
| 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 |