spinBayes: Semi-Parametric Gene-Environment Interaction via Bayesian Variable Selection

Many complex diseases are known to be affected by the interactions between genetic variants and environmental exposures beyond the main genetic and environmental effects. Existing Bayesian methods for gene-environment (G×E) interaction studies are challenged by the high-dimensional nature of the study and the complexity of environmental influences. We have developed a novel and powerful semi-parametric Bayesian variable selection method that can accommodate linear and nonlinear G×E interactions simultaneously (Ren et al. (2020) <doi:10.1002/sim.8434>). Furthermore, the proposed method can conduct structural identification by distinguishing nonlinear interactions from main effects only case within Bayesian framework. Spike-and-slab priors are incorporated on both individual and group level to shrink coefficients corresponding to irrelevant main and interaction effects to zero exactly. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently implemented in C++.

Version: 0.2.1
Depends: R (≥ 4.0.0)
Imports: Rcpp, splines, glmnet, utils, stats, ggplot2
LinkingTo: Rcpp, RcppArmadillo, testthat
Suggests: testthat (≥ 3.0.0), covr
Published: 2024-03-12
DOI: 10.32614/CRAN.package.spinBayes
Author: Jie Ren, Fei Zhou, Xiaoxi Li, Cen Wu, Yu Jiang
Maintainer: Jie Ren <jieren at ksu.edu>
BugReports: https://github.com/jrhub/spinBayes/issues
License: GPL-2
URL: https://github.com/jrhub/spinBayes
NeedsCompilation: yes
Materials: README
CRAN checks: spinBayes results


Reference manual: spinBayes.pdf


Package source: spinBayes_0.2.1.tar.gz
Windows binaries: r-devel: spinBayes_0.2.1.zip, r-release: spinBayes_0.2.1.zip, r-oldrel: spinBayes_0.2.1.zip
macOS binaries: r-release (arm64): spinBayes_0.2.1.tgz, r-oldrel (arm64): spinBayes_0.2.1.tgz, r-release (x86_64): spinBayes_0.2.1.tgz, r-oldrel (x86_64): spinBayes_0.2.1.tgz
Old sources: spinBayes archive


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