qvalue

DOI: 10.18129/B9.bioc.qvalue    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see qvalue.

Q-value estimation for false discovery rate control

Bioconductor version: 3.7

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 with contributions from Andrew J. Bass, Alan Dabney and David Robinson

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

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")

 

PDF	R Script	qvalue Package
PDF		Reference Manual
Text		NEWS

Details

biocViews	MultipleComparisons, Software
Version	2.12.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 13.5 years)
License	LGPL
Depends	R (>= 2.10)
Imports	splines, ggplot2, grid, reshape2
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL	http://github.com/jdstorey/qvalue
Depends On Me	anota, CancerMutationAnalysis, ChimpHumanBrainData, DEGseq, DrugVsDisease, metaseqR, prot2D, r3Cseq, SSPA, webbioc
Imports Me	Anaquin, anota, anota2seq, ChAMP, clusterProfiler, derfinder, DOSE, edge, erccdashboard, IHWpaper, InTAD, methylKit, msmsTests, MWASTools, netresponse, normr, OPWeight, Rnits, SDAMS, sights, sRAP, subSeq, synapter, trigger, webbioc
Suggests Me	biobroom, LBE, maanova, PREDA, RNAinteractMAPK, RnBeads, SummarizedBenchmark
Links To Me
Build Report

Package Archives

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

Source Package	qvalue_2.12.0.tar.gz
Windows Binary	qvalue_2.12.0.zip
Mac OS X 10.11 (El Capitan)	qvalue_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/qvalue
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/qvalue
Package Short Url	http://bioconductor.org/packages/qvalue/
Package Downloads Report	Download Stats