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-4.5)bayefdr_0.2.0.zip(r-4.4)bayefdr_0.2.0.zip(r-4.3)
bayefdr_0.2.0.tgz(r-4.4-any)bayefdr_0.2.0.tgz(r-4.3-any)
bayefdr_0.2.0.tar.gz(r-4.5-noble)bayefdr_0.2.0.tar.gz(r-4.4-noble)
bayefdr_0.2.0.tgz(r-4.4-emscripten)bayefdr_0.2.0.tgz(r-4.3-emscripten)
bayefdr.pdf |bayefdr.html✨
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 3 years agofrom:319682517c. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 12 2024 |
R-4.5-win | OK | Nov 12 2024 |
R-4.5-linux | OK | Nov 12 2024 |
R-4.4-win | OK | Nov 12 2024 |
R-4.4-mac | OK | Nov 12 2024 |
R-4.3-win | OK | Nov 12 2024 |
R-4.3-mac | OK | Nov 12 2024 |
Exports:cumplotefdrefdr_searchefnroptimaltraceplot
Dependencies:assertthatbase64encbslibcachemclicolorspacecolourpickercommonmarkcowplotcrayondigestevaluatefansifarverfastmapfontawesomefsggExtraggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimeminiUImunsellnlmepillarpkgconfigplyrpromisesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownsassscalesshinyshinyjssourcetoolsstringistringrtibbletinytexutf8vctrsviridisLitewithrxfunxtableyaml
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 |