ggmix: Variable Selection in Linear Mixed Models for SNP Data

Fit penalized multivariable linear mixed models with a single random effect to control for population structure in genetic association studies. The goal is to simultaneously fit many genetic variants at the same time, in order to select markers that are independently associated with the response. Can also handle prior annotation information, for example, rare variants, in the form of variable weights. For more information, see the website below and the accompanying paper: Bhatnagar et al., "Simultaneous SNP selection and adjustment for population structure in high dimensional prediction models", 2020, <doi:10.1101/408484>.

Version: 0.0.1
Depends: R (≥ 3.4.0)
Imports: glmnet, methods, stats, MASS, Matrix
Suggests: RSpectra, popkin, bnpsd, testthat, covr, knitr, rmarkdown
Published: 2020-03-20
Author: Sahir Bhatnagar [aut, cre] (https://sahirbhatnagar.com/), Karim Oualkacha [aut] (http://karimoualkacha.uqam.ca/), Yi Yang [aut] (http://www.math.mcgill.ca/yyang/), Celia Greenwood [aut] (http://www.mcgill.ca/statisticalgenetics/)
Maintainer: Sahir Bhatnagar <sahir.bhatnagar at gmail.com>
BugReports: https://github.com/sahirbhatnagar/ggmix/issues
License: MIT + file LICENSE
URL: https://github.com/sahirbhatnagar/ggmix
NeedsCompilation: no
Materials: README NEWS
CRAN checks: ggmix results

Downloads:

Reference manual: ggmix.pdf
Vignettes: Alternative Inputs for Population Structure
Introduction to the ggmix package
Incorporating Prior Annotation Weights
Package source: ggmix_0.0.1.tar.gz
Windows binaries: r-devel: ggmix_0.0.1.zip, r-devel-gcc8: ggmix_0.0.1.zip, r-release: ggmix_0.0.1.zip, r-oldrel: not available
OS X binaries: r-release: ggmix_0.0.1.tgz, r-oldrel: not available

Linking:

Please use the canonical form https://CRAN.R-project.org/package=ggmix to link to this page.