ashr

Methods for Adaptive Shrinkage, using Empirical Bayes

Matthew Stephens, Nan Xiao, Jason Willwerscheid, Mengyin Lu, David Gerard, Peter Carbonetto, Lei Sun

Last update: 21 August 2023

Copyright license: GNU General Public License

Software version identifier: 2.2-54, 2.0.5, 2.2-7, 2.2-32, 2.2-39, 2.2-40, 2.2-47, 2.2-63

Source code repository: https://github.com/cran/ashr

Description

The R package 'ashr' implements an Empirical Bayes approach for large-scale hypothesis testing and false discovery rate (FDR) estimation based on the methods proposed in M. Stephens, 2016, "False discovery rates: a new deal", <doi:10.1093/biostatistics/kxw041>. These methods can be applied whenever two sets of summary statistics—estimated effects and standard errors—are available, just as 'qvalue' can be applied to previously computed p-values. Two main interfaces are provided: ash(), which is more user-friendly; and ash.workhorse(), which has more options and is geared toward advanced users. The ash() and ash.workhorse() also provides a flexible modeling interface that can accommodate a variety of likelihoods (e.g., normal, Poisson) and mixture priors (e.g., uniform, normal).

Cites work

False discovery rates: a new deal