Documentation and vignettes are available here.
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")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.
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.
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 |
The flashier R package was developed by Jason Willwerscheid, Peter Carbonetto and Matthew Stephens, with many other contributors.