Package: qvalue 2.37.0
John D. Storey
qvalue: Q-value estimation for false discovery rate control
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.
Authors:
qvalue_2.37.0.tar.gz
qvalue_2.37.0.zip(r-4.5)qvalue_2.37.0.zip(r-4.4)qvalue_2.37.0.zip(r-4.3)
qvalue_2.37.0.tgz(r-4.4-any)qvalue_2.37.0.tgz(r-4.3-any)
qvalue_2.37.0.tar.gz(r-4.5-noble)qvalue_2.37.0.tar.gz(r-4.4-noble)
qvalue_2.37.0.tgz(r-4.4-emscripten)qvalue_2.37.0.tgz(r-4.3-emscripten)
qvalue.pdf |qvalue.html✨
qvalue/json (API)
NEWS
| # Install 'qvalue' in R: |
| install.packages('qvalue', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jdstorey/qvalue/issues
- hedenfalk - P-values and test-statistics from the Hedenfalk et al. (2001) gene expression dataset
On BioConductor:qvalue-2.37.0(bioc 3.20)qvalue-2.36.0(bioc 3.19)
Last updated 2 months agofrom:e517ebf612
Exports:empPvalslfdrpi0estqvaluewrite.qvalue
Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate p-values from a set of observed test statistics and simulated null test statistics | empPvals |
| P-values and test-statistics from the Hedenfalk et al. (2001) gene expression dataset | hedenfalk |
| Histogram of p-values | hist, hist.qvalue |
| Estimate local False Discovery Rate (FDR) | lfdr |
| Proportion of true null p-values | pi0est |
| Plotting function for q-value object | plot, plot.qvalue |
| Estimate the q-values for a given set of p-values | qvalue |
| Display q-value object | summary, summary.qvalue |
| Write results to file | write.qvalue |
