False Discovery Rate Analysis in R

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Overview:

This is a list intended to facilitate "comparison shopping" of R software for False Discovery Rate analysis, with links to the respective home pages and a short description of features.

Abbreviations:

FDR:generic term for a False Discovery Rate
Fdr:tail area based FDR, q-value
fdr:density-based local FDR

Please email Korbinian Strimmer if there are any inaccuracies, or to suggest additional packages.

Package Type of FDR Input Data Miscellaneous Package Authors
fdrtool fdr and Fdr simultaneously. p-values, z-scores, correlations, and t-scores. Modified Grenander density estimator. Truncated ML fit of empirical null model. K. Strimmer
mixfdr fdr and Fdr simultaneously. z-scores. Density estimation using normal mixtures. O. Muralidharan, with many suggestions from B. Efron
BUM / SPLOSH fdr and Fdr simultaneously. p-values. ML fit of parametric model. S. Pounds
SAGx fdr and Fdr simultaneously. p-values. Grenander density estimation. P. Broberg
qvalue frequentist Fdr. p-values. Truncated ML. Various methods for determining optimal truncation point. A. Dabney and J. D. Storey
fdrci frequentist Fdr. p-values. Permutation-based estimator (including pi0) as well as Fdr confidence intervals. J. Millstein
nFDR frequentist Fdr. p-values. Density estimator using Bernstein polynomials. M. Guedj and G. Nuel
multtest frequentist Fdr. p-values. Benjamini-Hochberg algorithm. K. S. Pollard, Y. Ge, S. Taylor, S. Dudoit
LBE frequentist Fdr. p-values. Location-based estimator. C. Dalmasso
FDR-AME frequentist Fdr. p-values. Benjamini-Hochberg and related algorithms. Y. Benjamini, E. Kenigsberg, A.t Reiner, D. Yekutieli
locfdr local fdr. z-scores. Density estimation via Poisson regression. Truncated ML fit of empirical null model. B. Efron, B. B. Turnbull and B. Narasimhan
nomi local fdr. z-scores. Normal mixture modeling of non-null density. G. McLachlan, R. W. Bean and L. B.-T. Jones
LocalFDR local fdr. p-values. Uses LOESS smoothing. J. Aubert
kerfdr local fdr. p-values. Kernel density estimator. M. Guedj and G. Nuel
twilight local fdr. p-values. KS fit of truncation point. S. Scheid
localFDR local fdr. p-values. Uses a stochastic order model. J.G. Liao
R script -
(fits null model but doesn't compute FDR)
z-scores. Characteristic function approach for fitting empirical null. J. Jin and T. Cai

 

Last modified:
October 12, 2013

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