qvalue
Q-value estimation for false discovery rate control
Bioconductor version: Release (3.20)
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("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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MultipleComparisons, Software |
| Version | 2.38.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19.5 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 | DEGseq, DrugVsDisease, anota, r3Cseq, webbioc, BonEV, cp4p, isva, ReAD, STAREG |
| Imports Me | Anaquin, CTSV, DOSE, DegCre, EventPointer, FindIT2, MOMA, MWASTools, OPWeight, PAST, RNAsense, RiboDiPA, Rnits, RolDE, SDAMS, SpaceMarkers, anota, clusterProfiler, derfinder, edge, erccdashboard, fishpond, metaseqR2, methylKit, msmsTests, netresponse, normr, sights, signatureSearch, subSeq, synapter, trigger, vsclust, webbioc, IHWpaper, AEenrich, cancerGI, fdrDiscreteNull, glmmSeq, groupedSurv, HDMT, jaccard, medScan, MetAlyzer, MOCHA, NBPSeq, qch, SeqFeatR, shinyExprPortal, ssizeRNA, TFactSR |
| Suggests Me | LBE, PREDA, RnBeads, biobroom, swfdr, RNAinteractMAPK, BootstrapQTL, dartR, dartR.base, dartR.popgen, DGEobj.utils, easylabel, familiar, jackstraw, 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_2.38.0.tar.gz |
| Windows Binary (x86_64) | qvalue_2.38.0.zip |
| macOS Binary (x86_64) | qvalue_2.38.0.tgz |
| macOS Binary (arm64) | qvalue_2.38.0.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 |