qvalue
Bioc currentQ-value estimation for false discovery rate control
Release Lineage
Entered 1.4 · May 17, 2004
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
9 5 exported
Complexity
5.6 avg / 12 max
Call network
9 nodes / 4 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
2,021
Files
30
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
4
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.10
System requirements
–
C++ standard
–
License
LGPL
License flags
not SPDX, not OSI
History
Versions
45
First release
2004-08-23
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
12
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 9
- Examples that run
- 100%9 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 93%
- Return-value docs
- 100%
- Help pages citing references
- 89%
- qvalue Package PDF
Repository practices
Checks run against github.com/jdstorey/qvalue on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| hedenfalk | list | 3 elements | No other package |
Topics
Depended on by (73)
Show 73 packagesHide 73 packages
Bioconductor (55)
CRAN (18)
People
- John D. Storey author maintainer
- Andrew J. Bass author
- Alan Dabney author
- David Robinson author
- Gregory Warnes contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("qvalue")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.