Package: bayefdr 0.2.0
bayefdr: Bayesian Estimation and Optimisation of Expected False Discovery Rate
Implements the Bayesian FDR control described by Newton et al. (2004), <doi:10.1093/biostatistics/5.2.155>. Allows optimisation and visualisation of expected error rates based on tail posterior probability tests. Based on code written by Catalina Vallejos for BASiCS, see Beyond comparisons of means: understanding changes in gene expression at the single-cell level Vallejos et al. (2016) <doi:10.1186/s13059-016-0930-3>.
Authors:
bayefdr_0.2.0.tar.gz
bayefdr_0.2.0.zip(r-4.7)bayefdr_0.2.0.zip(r-4.6)bayefdr_0.2.0.zip(r-4.5)
bayefdr_0.2.0.tgz(r-4.6-any)bayefdr_0.2.0.tgz(r-4.5-any)
bayefdr_0.2.0.tar.gz(r-4.7-any)bayefdr_0.2.0.tar.gz(r-4.6-any)
bayefdr_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
bayefdr/json (API)
NEWS
| # Install 'bayefdr' in R: |
| install.packages('bayefdr', repos = c('https://vallejosgroup.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/vallejosgroup/bayefdr/issues
Last updated from:319682517c. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 154 | ||
| source / vignettes | OK | 158 | ||
| linux-release-x86_64 | OK | 131 | ||
| macos-release-arm64 | OK | 147 | ||
| macos-oldrel-arm64 | OK | 191 | ||
| windows-devel | OK | 102 | ||
| windows-release | OK | 84 | ||
| windows-oldrel | OK | 93 | ||
| wasm-release | OK | 122 |
Exports:cumplotefdrefdr_searchefnroptimaltraceplot
Dependencies:assertthatbase64encbslibcachemclicolourpickercommonmarkcowplotcpp11digestevaluatefarverfastmapfontawesomefsggExtraggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlifecyclemagrittrmemoisemimeminiUIotelplyrpromisesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS7sassscalesshinyshinyjssourcetoolsstringistringrtinytexvctrsviridisLitewithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The 'nibbles' package. | bayefdr-package bayefdr |
| Plot the cumulative median, mean, and 95% high posterior density region. | cumplot |
| EFDR and EFNR estimation | efdr efnr |
| Bayesian EFDR optimisation. | efdr_search |
| Retrieve the index of the optimal probability threshold. | optimal |
| Plot the EFDR, EFNR grids of a bayefdr object. | plot.bayefdr |
| Print methods for bayefdr objects. | head.bayefdr print.bayefdr |
| Trace, marginal density histogram, and autocorrelation plot of MCMC draws. | traceplot |
