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qvalue

Q-value estimation for false discovery rate control


Bioconductor version: Release (3.19)

This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

Author: John D. Storey [aut, cre], Andrew J. Bass [aut], Alan Dabney [aut], David Robinson [aut], Gregory Warnes [ctb]

Maintainer: John D. Storey <jstorey at princeton.edu>, Andrew J. Bass <ajbass at emory.edu>

Citation (from within R, enter citation("qvalue")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("qvalue")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("qvalue")
qvalue Package PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews MultipleComparisons, Software
Version 2.36.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License LGPL
Depends R (>= 2.10)
Imports splines, ggplot2, grid, reshape2
System Requirements
URL http://github.com/jdstorey/qvalue
See More
Suggests knitr
Linking To
Enhances
Depends On Me anota, DEGseq, DrugVsDisease, r3Cseq, webbioc, BonEV, cp4p, isva, ReAD, STAREG
Imports Me Anaquin, anota, clusterProfiler, CTSV, derfinder, DOSE, edge, erccdashboard, EventPointer, FindIT2, fishpond, metaseqR2, methylKit, MOMA, msmsTests, MWASTools, netresponse, normr, OPWeight, PAST, RiboDiPA, RNAsense, Rnits, RolDE, SDAMS, sights, signatureSearch, SpaceMarkers, subSeq, synapter, trigger, vsclust, webbioc, IHWpaper, AEenrich, cancerGI, fdrDiscreteNull, glmmSeq, groupedSurv, HDMT, jaccard, jackstraw, medScan, MetAlyzer, MOCHA, NBPSeq, qch, SeqFeatR, shinyExprPortal, ssizeRNA, TFactSR
Suggests Me biobroom, LBE, PREDA, RnBeads, swfdr, RNAinteractMAPK, BootstrapQTL, CpGassoc, dartR, dartR.base, dartR.popgen, DGEobj.utils, easylabel, familiar, mutoss, Rediscover, seqgendiff, volcano3D, wrMisc
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package qvalue_2.36.0.tar.gz
Windows Binary qvalue_2.36.0.zip
macOS Binary (x86_64) qvalue_2.36.0.tgz
macOS Binary (arm64) qvalue_2.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/qvalue
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/qvalue
Bioc Package Browser https://code.bioconductor.org/browse/qvalue/
Package Short Url https://bioconductor.org/packages/qvalue/
Package Downloads Report Download Stats