fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

TLDR

False discovery rate methods are essential for high‑dimensional genomic and proteomic studies, and the R package ‘fdrtool’ provides comprehensive procedures for such analyses. fdrtool accepts diverse test statistics, simultaneously estimates local and tail‑area FDR, fits empirical null models to account for dispersion, offers interpretable graphics, and scales to millions of hypotheses with a unified estimation scheme. The program is freely available from CRAN under the GNU GPL v3, and can be contacted at strimmer@uni‑leipzig.de.

Abstract

Abstract Summary: False discovery rate (FDR) methodologies are essential in the study of high-dimensional genomic and proteomic data. The R package ‘fdrtool’ facilitates such analyses by offering a comprehensive set of procedures for FDR estimation. Its distinctive features include: (i) many different types of test statistics are allowed as input data, such as P-values, z-scores, correlations and t-scores; (ii) simultaneously, both local FDR and tail area-based FDR values are estimated for all test statistics and (iii) empirical null models are fit where possible, thereby taking account of potential over- or underdispersion of the theoretical null. In addition, ‘fdrtool’ provides readily interpretable graphical output, and can be applied to very large scale (in the order of millions of hypotheses) multiple testing problems. Consequently, ‘fdrtool’ implements a flexible FDR estimation scheme that is unified across different test statistics and variants of FDR. Availability: The program is freely available from the Comprehensive R Archive Network (http://cran.r-project.org/) under the terms of the GNU General Public License (version 3 or later). Contact: [e-mail]