To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("qvalue")
In most cases, you don't need to download the package archive at all.
qvalue
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This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see qvalue.
Q-value estimation for false discovery rate control
Bioconductor version: 3.1
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 Storey [aut, cre], Andrew Bass [ctb], Alan Dabney [ctb], David Robinson [ctb]
Maintainer: John D. Storey <jstorey at princeton.edu>
Citation (from within R,
enter citation("qvalue")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("qvalue")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("qvalue")
| R Script | qvalue Package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | MultipleComparisons, Software |
| Version | 2.0.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 11 years) |
| License | LGPL |
| Depends | R (>= 2.10) |
| Imports | splines, ggplot2, grid, reshape2 |
| LinkingTo | |
| Suggests | knitr |
| SystemRequirements | |
| Enhances | |
| URL | http://qvalue.princeton.edu/ http://github.com/jdstorey/qvalue |
| Depends On Me | anota, CancerMutationAnalysis, ChimpHumanBrainData, DEGseq, DrugVsDisease, metaseqR, prot2D, r3Cseq, SSPA, webbioc |
| Imports Me | anota, clusterProfiler, derfinder, DOSE, edge, erccdashboard, msmsTests, netresponse, Rnits, sRAP, synapter, trigger, webbioc |
| Suggests Me | LBE, maanova, PREDA, RNAinteractMAPK |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | qvalue_2.0.0.tar.gz |
| Windows Binary | qvalue_2.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | qvalue_2.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | qvalue_2.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/qvalue/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/qvalue/ |
| Package Downloads Report | Download Stats |
Documentation »
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