COBRAData-class         'COBRAData' object and constructor
COBRAPerformance-class
                        'COBRAPerformance' object and constructor
COBRAPlot-class         'COBRAPlot' object and constructor
COBRAapp                Interactive shiny app to visualize results
Extract                 Subsetting 'COBRAData', 'COBRAPerformance' or
                        'COBRAPlot' objects
basemethods             Accessor function for basemethods
calculate_adjp          Calculate adjusted p-values
calculate_performance   Calculate performance measures
cobradata_example       Example data set with three differential gene
                        expression methods
cobradata_example_sval
                        Example data set with three differential gene
                        expression methods
coerce                  Convert an object to another class
corr                    Accessor and replacement functions for 'corr'
                        slot
deviation               Accessor and replacement functions for
                        'deviation' slot
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
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
plotcolors              Accessor and replacement functions for
                        'plotcolors' slot
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 format
update_cobraperformance
                        Update 'COBRAPerformance' or 'COBRAPlot' object
                        to the current version of the class format
