qvalue: Q-value estimation for false discovery rate control
Version 2.8.0

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.

AuthorJohn D. Storey with contributions from Andrew J. Bass, Alan Dabney and David Robinson
Bioconductor views MultipleComparisons
Date of publicationNone
MaintainerJohn D. Storey <jstorey@princeton.edu>, Andrew J. Bass <ajbass@princeton.edu>
LicenseLGPL
Version2.8.0
URL http://github.com/jdstorey/qvalue
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("qvalue")

Getting started

README.md

Popular man pages

empPvals: Calculate p-values from a set of observed test statistics and...
hedenfalk: P-values and test-statistics from the Hedenfalk et al. (2001)...
hist.qvalue: Histogram of p-values
lfdr: Estimate local False Discovery Rate (FDR)
plot.qvalue: Plotting function for q-value object
qvalue: Estimate the q-values for a given set of p-values
summary.qvalue: Display q-value object
See all...

All man pages Function index File listing

Man pages

empPvals: Calculate p-values from a set of observed test statistics and...
hedenfalk: P-values and test-statistics from the Hedenfalk et al. (2001)...
hist.qvalue: Histogram of p-values
lfdr: Estimate local False Discovery Rate (FDR)
pi0est: Proportion of true null p-values
plot.qvalue: Plotting function for q-value object
qvalue: Estimate the q-values for a given set of p-values
summary.qvalue: Display q-value object
write.qvalue: Write results to file

Functions

empPvals Man page Source code
hedenfalk Man page
hist, Man page
hist.qvalue Man page Source code
lfdr Man page Source code
multiplot Source code
pi0est Man page Source code
plot, Man page
plot.qvalue Man page Source code
qvalue Man page Source code
summary, Man page
summary.qvalue Man page Source code
write.qvalue Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/empPvals.R
R/hedenfalk.R
R/hist_qvalue.R
R/lfdr.R
R/multiplot.R
R/pi0est.R
R/plot_qvalue.R
R/qvalue.R
R/summary_qvalue.R
R/write_qvalue.R
README.md
build
build/vignette.rds
data
data/datalist
data/hedenfalk.RData
inst
inst/NEWS
inst/doc
inst/doc/qvalue.R
inst/doc/qvalue.Rnw
inst/doc/qvalue.pdf
man
man/empPvals.Rd
man/hedenfalk.Rd
man/hist.qvalue.Rd
man/lfdr.Rd
man/pi0est.Rd
man/plot.qvalue.Rd
man/qvalue.Rd
man/summary.qvalue.Rd
man/write.qvalue.Rd
vignettes
vignettes/qvalue.Rnw
vignettes/qvaluerefs.bib
qvalue documentation built on May 20, 2017, 9:15 p.m.

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