README.md

In willwerscheid/flashier: Empirical Bayes Matrix Factorization

flashier

Documentation and vignettes are available here.

Quick start

Install the latest version of flashier from GitHub:

install.packages("remotes")
remotes::install_github("willwerscheid/flashier")

Once you have installed the package, load the package in R:

library(flashier)

Next, run an example analysis of the GTEx data set:

data(gtex)
fl <- flash(gtex,greedy_Kmax = 3,backfit = TRUE)

For a more detailed introduction to flashier, see the introductory vignette and, later, the other vignettes.

To learn more, visit the package website, and view the "flash" help page in R:

help("flash")

Citing this work

If you find the flashier package or any of the source code in this repository useful for your work, please cite:

Jason Willwerscheid, Peter Carbonetto and Matthew Stephens. ebnm: an R package for solving the empirical Bayes normal means problem using a variety of prior families. arXiv:2110.00152.

License

Copyright (c) 2018-2024, Jason Willwerscheid, Peter Carbonetto and Matthew Stephens.

All source code and software in this repository are made available under the terms of the MIT license.

Notes

Please note that function names changed in flashier version 0.2.44. If you are using flashier code from previous versions, please make the following substitutions, and note that many parameter names have changed as well:

Old Name | New Name --- | --- as.ebnm.fn | flash_ebnm conv.crit.elbo | flash_conv_crit_elbo_diff conv.crit.factors | flash_conv_crit_max_chg_F conv.crit.loadings | flash_conv_crit_max_chg_L display.elbo | flash_verbose_elbo display.elbo.diff | flash_verbose_elbo_diff display.F.max.chg | flash_verbose_max_chg_F display.L.max.chg | flash_verbose_max_chg_L display.max.chg | flash_verbose_max_chg ff.elbo | flash_fit_get_elbo ff.est.tau | flash_fit_get_est_tau ff.fixed.tau | flash_fit_get_fixed_tau ff.g | flash_fit_get_g ff.KL | flash_fit_get_KL ff.p2m | flash_fit_get_p2m ff.pm | flash_fit_get_pm ff.tau | flash_fit_get_tau flash.add.greedy | flash_greedy flash.backfit | flash_backfit flash.fit | flash_fit flash.fix.factors | flash_factors_fix flash.init | flash_init flash.init.factors | flash_factors_init flash.nullcheck | flash_nullcheck flash.remove.factors | flash_factors_remove flash.reorder.factors | flash_factors_reorder flash.set.factors.to.zero | flash_factors_set_to_zero flash.set.verbose | flash_set_verbose init.fn.default | flash_greedy_init_default init.fn.irlba | flash_greedy_init_irlba init.fn.softImpute | flash_greedy_init_softImpute

Credits

The flashier R package was developed by Jason Willwerscheid, Peter Carbonetto and Matthew Stephens, with many other contributors.

willwerscheid/flashier documentation built on Jan. 30, 2025, 11:27 p.m.