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Bioinformatics Advance Access originally published online on April 25, 2008
Bioinformatics 2008 24(12):1461-1462; doi:10.1093/bioinformatics/btn209
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Korbinian Strimmer

Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany


  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: strimmer{at}uni-leipzig.de

Associate Editor: Trey Ideker

Received on December 12, 2007; revised on January 28, 2008; accepted on April 23, 2008

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