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mvsusieR

Continuous Integration

Implements a multivariate generalization of the “Sum of Single Effects” (SuSiE) model for variable selection in multivariate linear regression. Go here for documentation and tutorials.

Setup

To install the latest version of the mvsusieR package from GitHub, run the following code in R:

install.packages("remotes")
library(remotes)
install_github("stephenslab/mvsusieR")

This command should automatically install all required packages if they are not installed already.

Note that mvsusieR uses mashr, which in turn requires the GNU Scientific libraries (GSL). You may want to install mashr first before attempting to install mvsusieR.

Developer notes

  • When any changes are made to roxygen2 markup, simply run devtools::document() to update package NAMESPACE and documentation files.

  • To install and test the package, run the following commands in the shell:

    VERSION=`grep Version DESCRIPTION | awk '{print $2}'`
R CMD build --resave-data --no-build-vignettes mvsusieR
R CMD INSTALL mvsusieR_$VERSION.tar.gz
R CMD check --as-cran --ignore-vignettes mvsusieR_$VERSION.tar.gz

  • Run pkgdown::build_site() to build the pkgdown site.

  • To format R codes in the R folder,

    for i in `ls R/*.R`; do bash inst/misc/format_r_code.sh $i; done