flashr: Empirical Bayes Factor Analysis in R

Methods for matrix factorization based on Empirical Bayes Matrix Factorization. The name of the package, "flashr," comes from "Factors and Loadings by Adaptive SHrinkage in R".

Important note

We are no longer supporting or developing flashr: we have switched to supporting a replacement R package, flashier, which contains most of the features of flashr, plus many important improvements, including a new, user-friendly interface, more modeling options, faster algorithms, and more detailed statistical outputs. Please use flashier rather than flashr!

License

Copyright (c) 2017-2018, Matthew Stephens and Wei Wang.

All source code and software in this repository are made available under the terms of the BSD 3-Clause License. See the LICENSE file for the full text of the license.

Citing this work

If you find that this R package is useful for your work, please cite our paper:

W. Wang and M. Stephens, 2018. Empirical Bayes matrix factorization. arXiv:1802.06931.

Quick start

Follow these steps to quickly get started using flashr.

1. Install the flashr using devtools. Please note that it can take several minutes to build the vignettes:

   install.packages("devtools")
   library(devtools)
   install_github("stephenslab/flashr",build_vignettes = TRUE)

   This command should automatically retrieve and install the ashr and ebnm packages from GitHub (and possibly other packages). If it does not, install ashr and ebnm separately using devtools:

   install_github("stephens999/ashr")
   install_github("stephenslab/ebnm")

   Note: If you are interested in attempting to reproduce the results in the Wang and Stephens (2018) manuscript, the flashr release that most closely matches the package used in the paper is version 0.4-10. This release can be installed by running the following in R:

   install_github("stephenslab/[email protected]")

2. Optionally, install MOSEK and the Rmosek package, for faster model fitting. See the ashr GitHub repository for details.

3. Run a few toy examples illustrating the flash function:

   example("flash")

4. Explore the introductory flashr vignette:

   vignette("flash_intro")

5. Explore the vignette illustrating some more advanced features of flashr:

   vignette("flash_advanced")

6. See the online documentation to learn more about the flashr package.

Developer notes

• Run pkgdown::build_site(mathjax = FALSE) in R to build the website using pkgdown. Make sure you are connected to the Internet while running these commands.

Credits

This software was developed by Matthew Stephens, Wei Wang, Jason Willwerscheid and Peter Carbonetto at the University of Chicago.