Package: BG2 1.13.0

Jacob Williams

BG2: Performs Bayesian GWAS analysis for non-Gaussian data using BG2

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.

Authors:Jacob Williams [aut, cre], Shuangshuang Xu [aut], Marco Ferreira [aut]

BG2_1.13.0.tar.gz
BG2_1.13.0.zip(r-4.7)BG2_1.13.0.zip(r-4.6)BG2_1.13.0.zip(r-4.5)
BG2_1.13.0.tgz(r-4.6-any)BG2_1.13.0.tgz(r-4.5-any)
BG2_1.13.0.tar.gz(r-4.7-any)BG2_1.13.0.tar.gz(r-4.6-any)
BG2_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
BG2/json (API)

# Install 'BG2' in R:

install.packages('BG2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

kinship - A. Thaliana Kinship matrix
SNPs - A. Thaliana Genotype matrix
Y_binary - A. Thaliana Simulated Phenotype matrix
Y_poisson - A. Thaliana Simulated Phenotype matrix

On BioConductor:BG2-1.13.0(bioc 3.24)BG2-1.12.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bayesian assaydomain snp genomewideassociation

4.00 score 3 scripts 1 exports 79 dependencies

Last updated from:23448c8758. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	178
linux-devel-x86_64	OK	280
source / vignettes	OK	328
linux-release-x86_64	OK	265
macos-release-arm64	OK	329
macos-oldrel-arm64	OK	288
windows-devel	OK	367
windows-release	OK	367
windows-oldrel	OK	357
wasm-release	OK	165

Exports:BG2

Dependencies:cachem caret class cli clock codetools cpp11 crayon data.table diagram digest dplyr e1071 farver fastmap foreach future future.apply GA generics ggplot2 globals glue gower gtable hardhat ipred isoband iterators KernSmooth labeling lattice lava lifecycle listenv lubridate magrittr MASS Matrix memoise ModelMetrics nlme nnet numDeriv parallelly pillar pkgconfig plyr pROC prodlim progressr proxy purrr R6 RColorBrewer Rcpp RcppArmadillo recipes reshape2 rlang rpart S7 scales shape sparsevctrs SQUAREM stringi stringr survival tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite withr

BG2

Rendered fromBG2.Rmdusingknitr::rmarkdown

Last update: 2023-01-08
Started: 2022-12-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Performs BG2 as described in the manuscript, Xu, Williams, and Ferreira BG2: Bayesian variable selection in generalized linear mixed models with non-local priors for non-Gaussian GWAS data, Bioinformatics, Submitted.	BG2
A. Thaliana Kinship matrix	kinship
A. Thaliana Genotype matrix	SNPs
A. Thaliana Simulated Phenotype matrix	Y_binary
A. Thaliana Simulated Phenotype matrix	Y_poisson