qvalue: Q-value estimation for false discovery rate control

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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
Date of publication
None
Maintainer
John D. Storey <jstorey@princeton.edu>, Andrew J. Bass <ajbass@princeton.edu>
License
LGPL
Version
2.6.0
URLs

View on Bioconductor

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

Files in this package

qvalue/DESCRIPTION
qvalue/NAMESPACE
qvalue/R
qvalue/R/empPvals.R
qvalue/R/hedenfalk.R
qvalue/R/hist_qvalue.R
qvalue/R/lfdr.R
qvalue/R/multiplot.R
qvalue/R/pi0est.R
qvalue/R/plot_qvalue.R
qvalue/R/qvalue.R
qvalue/R/summary_qvalue.R
qvalue/R/write_qvalue.R
qvalue/README.md
qvalue/build
qvalue/build/vignette.rds
qvalue/data
qvalue/data/datalist
qvalue/data/hedenfalk.RData
qvalue/inst
qvalue/inst/NEWS
qvalue/inst/doc
qvalue/inst/doc/qvalue.R
qvalue/inst/doc/qvalue.Rnw
qvalue/inst/doc/qvalue.pdf
qvalue/man
qvalue/man/empPvals.Rd
qvalue/man/hedenfalk.Rd
qvalue/man/hist.qvalue.Rd
qvalue/man/lfdr.Rd
qvalue/man/pi0est.Rd
qvalue/man/plot.qvalue.Rd
qvalue/man/qvalue.Rd
qvalue/man/summary.qvalue.Rd
qvalue/man/write.qvalue.Rd
qvalue/vignettes
qvalue/vignettes/qvalue.Rnw
qvalue/vignettes/qvaluerefs.bib