| basemethods | Accessor function for basemethods |
| calculate_adjp | Calculate adjusted p-values |
| calculate_performance | Calculate performance measures |
| COBRAapp | Interactive shiny app to visualize results |
| COBRAData | 'COBRAData' object and constructor |
| cobradata_example | Example data set with three differential gene expression... |
| cobradata_example_sval | Example data set with three differential gene expression... |
| COBRAPerformance | 'COBRAPerformance' object and constructor |
| COBRAPlot | 'COBRAPlot' object and constructor |
| coerce | Convert an object to another class |
| corr | Accessor and replacement functions for 'corr' slot |
| deviation | Accessor and replacement functions for 'deviation' slot |
| Extract | Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot'... |
| facetted | Accessor and replacement functions for 'facetted' slot |
| fdrnbr | Accessor and replacement functions for 'fdrnbr' slot |
| fdrnbrcurve | Accessor and replacement functions for 'fdrnbrcurve' slot |
| fdrtpr | Accessor and replacement functions for 'fdrtpr' slot |
| fdrtprcurve | Accessor and replacement functions for 'fdrtprcurve' slot |
| fpc | Accessor and replacement functions for 'fpc' slot |
| fpr | Accessor and replacement functions for 'fpr' slot |
| fsrnbr | Accessor and replacement functions for 'fsrnbr' slot |
| fsrnbrcurve | Accessor and replacement functions for 'fsrnbrcurve' slot |
| maxsplit | Accessor and replacement functions for 'maxsplit' slot |
| onlyshared | Accessor and replacement functions for 'onlyshared' slot |
| overlap | Accessor and replacement functions for 'overlap' slot |
| padj | Accessor and replacement functions for 'padj' slot |
| plotcolors | Accessor and replacement functions for 'plotcolors' slot |
| plot_corr | Plot correlations |
| plot_deviation | Plot deviations |
| plot_fdrnbrcurve | Plot number of significant features vs FDR |
| plot_fdrtprcurve | Plot TPR vs FDR |
| plot_fpc | Plot FP curves |
| plot_fpr | Plot FPR |
| plot_fsrnbrcurve | Plot number of features with s-value below threshold vs FSR |
| plot_overlap | Plot Venn diagram |
| plot_roc | Plot ROC curves |
| plot_scatter | Plot scatter plots |
| plot_tpr | Plot TPR |
| plot_upset | Create UpSet plots |
| prepare_data_for_plot | Prepare data for plotting |
| pval | Accessor and replacement functions for 'pval' slot |
| reorder_levels | Reorder levels in COBRAPlot object |
| roc | Accessor and replacement functions for 'roc' slot |
| scatter | Accessor and replacement functions for 'scatter' slot |
| score | Accessor and replacement functions for 'score' slot |
| splv | Accessor and replacement functions for 'splv' slot |
| stratiflevels | Accessor function for stratification levels |
| sval | Accessor and replacement functions for 'sval' slot |
| tpr | Accessor and replacement functions for 'tpr' slot |
| truth | Accessor and replacement functions for 'truth' slot |
| update_cobradata | Update 'COBRAData' object to the current version of the class... |
| update_cobraperformance | Update 'COBRAPerformance' or 'COBRAPlot' object to the... |
