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