Package: iCOBRA 1.35.0
Charlotte Soneson
iCOBRA: Comparison and Visualization of Ranking and Assignment Methods
This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. Various types of performance plots can be generated programmatically. The package also contains a shiny application for interactive exploration of results.
Authors:
iCOBRA_1.35.0.tar.gz
iCOBRA_1.35.0.zip(r-4.5)iCOBRA_1.35.0.zip(r-4.4)iCOBRA_1.33.0.zip(r-4.3)
iCOBRA_1.35.0.tgz(r-4.4-any)iCOBRA_1.33.0.tgz(r-4.3-any)
iCOBRA_1.35.0.tar.gz(r-4.5-noble)iCOBRA_1.35.0.tar.gz(r-4.4-noble)
iCOBRA_1.35.0.tgz(r-4.4-emscripten)iCOBRA_1.33.0.tgz(r-4.3-emscripten)
iCOBRA.pdf |iCOBRA.html✨
iCOBRA/json (API)
NEWS
| # Install 'iCOBRA' in R: |
| install.packages('iCOBRA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/csoneson/icobra/issues
- cobradata_example - Example data set with three differential gene expression methods
- cobradata_example_sval - Example data set with three differential gene expression methods
On BioConductor:iCOBRA-1.35.0(bioc 3.21)iCOBRA-1.34.0(bioc 3.20)
Last updated 2 months agofrom:c609c48e6e. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 03 2024 |
| R-4.5-win | NOTE | Dec 03 2024 |
| R-4.5-linux | NOTE | Dec 03 2024 |
| R-4.4-win | NOTE | Dec 03 2024 |
| R-4.4-mac | NOTE | Dec 03 2024 |
| R-4.3-win | NOTE | Sep 22 2024 |
| R-4.3-mac | NOTE | Sep 22 2024 |
Exports:.COBRAData.COBRAPerformance.COBRAPlotbasemethodscalculate_adjpcalculate_performanceCOBRAappCOBRADataCOBRAData_from_textCOBRAData_to_textCOBRAPerformanceCOBRAPlotcoercecorrcorr<-deviationdeviation<-facettedfacetted<-fdrnbrfdrnbr<-fdrnbrcurvefdrnbrcurve<-fdrtprfdrtpr<-fdrtprcurvefdrtprcurve<-fpcfpc<-fprfpr<-fsrnbrfsrnbr<-fsrnbrcurvefsrnbrcurve<-maxsplitmaxsplit<-onlysharedonlyshared<-overlapoverlap<-padjpadj<-plot_corrplot_deviationplot_fdrnbrcurveplot_fdrtprcurveplot_fpcplot_fprplot_fsrnbrcurveplot_overlapplot_rocplot_scatterplot_tprplot_upsetplotcolorsplotcolors<-prepare_data_for_plotpvalpval<-reorder_levelsrocroc<-scatterscatter<-scorescore<-splvsplv<-stratiflevelssvalsval<-tprtpr<-truthtruth<-update_cobradataupdate_cobraperformance
Dependencies:base64encbitopsbslibcachemcaToolsclicolorspacecommonmarkcrayoncrosstalkdigestdplyrDTevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegplotsgridExtragtablegtoolshighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelimmamagrittrmarkdownMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigplyrpromisesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownROCRsassscalesshinyshinyBSshinydashboardsourcetoolsstatmodstringistringrtibbletidyselecttinytexUpSetRutf8vctrsviridisLitewithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Accessor function for basemethods | basemethods basemethods,COBRAPerformance-method basemethods,COBRAPlot-method |
| Calculate adjusted p-values | calculate_adjp |
| Calculate performance measures | calculate_performance |
| Interactive shiny app to visualize results | COBRAapp |
| Example data set with three differential gene expression methods | cobradata_example |
| Example data set with three differential gene expression methods | cobradata_example_sval |
| 'COBRAData' object and constructor | .COBRAData COBRAData COBRAData-class COBRAData_from_text COBRAData_to_text |
| 'COBRAPerformance' object and constructor | .COBRAPerformance COBRAPerformance COBRAPerformance-class |
| 'COBRAPlot' object and constructor | .COBRAPlot COBRAPlot COBRAPlot-class |
| Convert an object to another class | COBRAPlot,COBRAPerformance-method coerce coerce, coerce,COBRAPerformance,COBRAPlot-method coerce,COBRAPlot,COBRAPerformance-method |
| Accessor and replacement functions for 'corr' slot | corr corr,COBRAPerformance-method corr,COBRAPlot-method corr<- corr<-,COBRAPerformance,data.frame-method corr<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'deviation' slot | deviation deviation,COBRAPerformance-method deviation,COBRAPlot-method deviation<- deviation<-,COBRAPerformance,data.frame-method deviation<-,COBRAPlot,data.frame-method |
| Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot' objects | Extract [ [,COBRAData-method [,COBRAPerformance-method [,COBRAPlot-method \S4method{[}{COBRAData,ANY,ANY,ANY} \S4method{[}{COBRAData,ANY,ANY} \S4method{[}{COBRAPerformance,ANY,ANY,ANY} \S4method{[}{COBRAPerformance,ANY,ANY} \S4method{[}{COBRAPlot,ANY,ANY,ANY} \S4method{[}{COBRAPlot,ANY,ANY} |
| Accessor and replacement functions for 'facetted' slot | facetted facetted,COBRAPlot-method facetted<- facetted<-,COBRAPlot,logical-method |
| Accessor and replacement functions for 'fdrnbr' slot | fdrnbr fdrnbr,COBRAPerformance-method fdrnbr,COBRAPlot-method fdrnbr<- fdrnbr<-,COBRAPerformance,data.frame-method fdrnbr<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'fdrnbrcurve' slot | fdrnbrcurve fdrnbrcurve,COBRAPerformance-method fdrnbrcurve,COBRAPlot-method fdrnbrcurve<- fdrnbrcurve<-,COBRAPerformance,data.frame-method fdrnbrcurve<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'fdrtpr' slot | fdrtpr fdrtpr,COBRAPerformance-method fdrtpr,COBRAPlot-method fdrtpr<- fdrtpr<-,COBRAPerformance,data.frame-method fdrtpr<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'fdrtprcurve' slot | fdrtprcurve fdrtprcurve,COBRAPerformance-method fdrtprcurve,COBRAPlot-method fdrtprcurve<- fdrtprcurve<-,COBRAPerformance,data.frame-method fdrtprcurve<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'fpc' slot | fpc fpc,COBRAPerformance-method fpc,COBRAPlot-method fpc<- fpc<-,COBRAPerformance,data.frame-method fpc<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'fpr' slot | fpr fpr,COBRAPerformance-method fpr,COBRAPlot-method fpr<- fpr<-,COBRAPerformance,data.frame-method fpr<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'fsrnbr' slot | fsrnbr fsrnbr,COBRAPerformance-method fsrnbr,COBRAPlot-method fsrnbr<- fsrnbr<-,COBRAPerformance,data.frame-method fsrnbr<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'fsrnbrcurve' slot | fsrnbrcurve fsrnbrcurve,COBRAPerformance-method fsrnbrcurve,COBRAPlot-method fsrnbrcurve<- fsrnbrcurve<-,COBRAPerformance,data.frame-method fsrnbrcurve<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'maxsplit' slot | maxsplit maxsplit,COBRAPerformance-method maxsplit,COBRAPlot-method maxsplit<- maxsplit<-,COBRAPerformance,numeric-method maxsplit<-,COBRAPlot,numeric-method |
| Accessor and replacement functions for 'onlyshared' slot | onlyshared onlyshared,COBRAPerformance-method onlyshared,COBRAPlot-method onlyshared<- onlyshared<-,COBRAPerformance,logical-method onlyshared<-,COBRAPlot,logical-method |
| Accessor and replacement functions for 'overlap' slot | overlap overlap,COBRAPerformance-method overlap,COBRAPlot-method overlap<- overlap<-,COBRAPerformance,list_df-method overlap<-,COBRAPlot,list_df-method |
| Accessor and replacement functions for 'padj' slot | padj padj,COBRAData-method padj<- padj<-,COBRAData,data.frame-method |
| Plot correlations | plot_corr |
| Plot deviations | plot_deviation |
| Plot number of significant features vs FDR | plot_fdrnbrcurve |
| Plot TPR vs FDR | plot_fdrtprcurve |
| Plot FP curves | plot_fpc |
| Plot FPR | plot_fpr |
| Plot number of features with s-value below threshold vs FSR | plot_fsrnbrcurve |
| Plot Venn diagram | plot_overlap |
| Plot ROC curves | plot_roc |
| Plot scatter plots | plot_scatter |
| Plot TPR | plot_tpr |
| Create UpSet plots | plot_upset |
| Accessor and replacement functions for 'plotcolors' slot | plotcolors plotcolors,COBRAPlot-method plotcolors<- plotcolors<-,COBRAPlot,character-method |
| Prepare data for plotting | prepare_data_for_plot |
| Accessor and replacement functions for 'pval' slot | pval pval,COBRAData-method pval<- pval<-,COBRAData,data.frame-method |
| Reorder levels in COBRAPlot object | reorder_levels |
| Accessor and replacement functions for 'roc' slot | roc roc,COBRAPerformance-method roc,COBRAPlot-method roc<- roc<-,COBRAPerformance,data.frame-method roc<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'scatter' slot | scatter scatter,COBRAPerformance-method scatter,COBRAPlot-method scatter<- scatter<-,COBRAPerformance,data.frame-method scatter<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'score' slot | score score,COBRAData-method score<- score<-,COBRAData,data.frame-method |
| Accessor and replacement functions for 'splv' slot | splv splv,COBRAPerformance-method splv,COBRAPlot-method splv<- splv<-,COBRAPerformance,character-method splv<-,COBRAPlot,character-method |
| Accessor function for stratification levels | stratiflevels stratiflevels,COBRAPerformance-method stratiflevels,COBRAPlot-method |
| Accessor and replacement functions for 'sval' slot | sval sval,COBRAData-method sval<- sval<-,COBRAData,data.frame-method |
| Accessor and replacement functions for 'tpr' slot | tpr tpr,COBRAPerformance-method tpr,COBRAPlot-method tpr<- tpr<-,COBRAPerformance,data.frame-method tpr<-,COBRAPlot,data.frame-method |
| Accessor and replacement functions for 'truth' slot | truth truth,COBRAData-method truth<- truth<-,COBRAData,data.frame-method |
| Update 'COBRAData' object to the current version of the class format | update_cobradata |
| Update 'COBRAPerformance' or 'COBRAPlot' object to the current version of the class format | update_cobraperformance |
