mvsusieR

Implements a multivariate generalization of the “Sum of Single Effects” (SuSiE) model for variable selection in multivariate linear regression (Y = XB + E, where Y is N x R). The methods are particularly well-suited to settings where some of the X variables are highly correlated, the true effects are sparse, and effects may be shared across multiple conditions (traits). A major motivation is multi-trait genetic fine-mapping, but the methods are applicable more generally.

Go here for documentation and tutorials.

Setup

To install the latest version of the mvsusieR package from GitHub:

# install.packages("remotes")
remotes::install_github("stephenslab/mvsusieR")

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

Note that mvsusieR depends on mashr, which requires the GNU Scientific Library (GSL). You may want to install mashr first before attempting to install mvsusieR.

Citing this work

If you find the mvsusieR package useful for your work, please cite:

Zou, Y., Carbonetto, P., Xie, D., Wang, G. & Stephens, M. (2026). Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model. Nature Genetics 58, 454-462. https://doi.org/10.1038/s41588-025-02486-7

Developer notes

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

• To install and test the package:

  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.