Package: iCOBRA 1.41.1

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:Charlotte Soneson [aut, cre]

iCOBRA_1.41.1.tar.gz
iCOBRA_1.41.1.zip(r-4.7)iCOBRA_1.41.1.zip(r-4.6)iCOBRA_1.41.1.zip(r-4.5)
iCOBRA_1.41.1.tgz(r-4.6-any)iCOBRA_1.41.1.tgz(r-4.5-any)
iCOBRA_1.41.1.tar.gz(r-4.7-any)iCOBRA_1.41.1.tar.gz(r-4.6-any)
iCOBRA_1.41.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iCOBRA/json (API)

# 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

Pkgdown/docs site:https://csoneson.github.io

Datasets:

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-1.41.1(bioc 3.24)iCOBRA-1.40.0(bioc 3.23)

classification visualization

9.08 score 16 stars 1 packages 279 scripts 704 downloads 5 mentions 78 exports 77 dependencies

Last updated from:88db646873. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	166
linux-devel-x86_64	NOTE	230
source / vignettes	OK	205
linux-release-x86_64	NOTE	286
macos-release-arm64	NOTE	141
macos-oldrel-arm64	NOTE	139
windows-devel	NOTE	182
windows-release	NOTE	163
windows-oldrel	NOTE	169
wasm-release	OK	129

Exports:.COBRAData .COBRAPerformance .COBRAPlot basemethods calculate_adjp calculate_performance COBRAapp COBRAData COBRAData_from_text COBRAData_to_text COBRAPerformance COBRAPlot coerce corr corr<-deviation deviation<-facetted facetted<-fdrnbr fdrnbr<-fdrnbrcurve fdrnbrcurve<-fdrtpr fdrtpr<-fdrtprcurve fdrtprcurve<-fpc fpc<-fpr fpr<-fsrnbr fsrnbr<-fsrnbrcurve fsrnbrcurve<-maxsplit maxsplit<-onlyshared onlyshared<-overlap overlap<-padj padj<-plot_corr plot_deviation plot_fdrnbrcurve plot_fdrtprcurve plot_fpc plot_fpr plot_fsrnbrcurve plot_overlap plot_roc plot_scatter plot_tpr plot_upset plotcolors plotcolors<-prepare_data_for_plot pval pval<-reorder_levels roc roc<-scatter scatter<-score score<-splv splv<-stratiflevels sval sval<-tpr tpr<-truth truth<-update_cobradata update_cobraperformance

Dependencies:base64enc bitops bslib cachem caTools cli commonmark cpp11 crosstalk digest dplyr DT evaluate farver fastmap fontawesome fs generics ggplot2 glue gplots gtable gtools highr htmltools htmlwidgets httpuv isoband jquerylib jsonlite KernSmooth knitr labeling later lazyeval lifecycle limma magrittr memoise mime otel patchwork pillar pkgconfig plyr promises prompter purrr R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown ROCR S7 sass scales shiny shinydashboard SimpleUpset sourcetools statmod stringi stringr tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun xtable yaml

iCOBRA User Guide

Rendered fromiCOBRA.Rmdusingknitr::rmarkdown

Last update: 2025-12-13
Started: 2015-11-25

Citation

Development and contributors

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	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