Man pages for iCOBRA
Comparison and Visualization of Ranking and Assignment Methods

basemethodsAccessor function for basemethods
calculate_adjpCalculate adjusted p-values
calculate_performanceCalculate performance measures
COBRAappInteractive shiny app to visualize results
COBRAData'COBRAData' object and constructor
cobradata_exampleExample data set with three differential gene expression...
cobradata_example_svalExample data set with three differential gene expression...
COBRAPerformance'COBRAPerformance' object and constructor
COBRAPlot'COBRAPlot' object and constructor
coerceConvert an object to another class
corrAccessor and replacement functions for 'corr' slot
deviationAccessor and replacement functions for 'deviation' slot
ExtractSubsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot'...
facettedAccessor and replacement functions for 'facetted' slot
fdrnbrAccessor and replacement functions for 'fdrnbr' slot
fdrnbrcurveAccessor and replacement functions for 'fdrnbrcurve' slot
fdrtprAccessor and replacement functions for 'fdrtpr' slot
fdrtprcurveAccessor and replacement functions for 'fdrtprcurve' slot
fpcAccessor and replacement functions for 'fpc' slot
fprAccessor and replacement functions for 'fpr' slot
fsrnbrAccessor and replacement functions for 'fsrnbr' slot
fsrnbrcurveAccessor and replacement functions for 'fsrnbrcurve' slot
maxsplitAccessor and replacement functions for 'maxsplit' slot
onlysharedAccessor and replacement functions for 'onlyshared' slot
overlapAccessor and replacement functions for 'overlap' slot
padjAccessor and replacement functions for 'padj' slot
plotcolorsAccessor and replacement functions for 'plotcolors' slot
plot_corrPlot correlations
plot_deviationPlot deviations
plot_fdrnbrcurvePlot number of significant features vs FDR
plot_fdrtprcurvePlot TPR vs FDR
plot_fpcPlot FP curves
plot_fprPlot FPR
plot_fsrnbrcurvePlot number of features with s-value below threshold vs FSR
plot_overlapPlot Venn diagram
plot_rocPlot ROC curves
plot_scatterPlot scatter plots
plot_tprPlot TPR
plot_upsetCreate UpSet plots
prepare_data_for_plotPrepare data for plotting
pvalAccessor and replacement functions for 'pval' slot
reorder_levelsReorder levels in COBRAPlot object
rocAccessor and replacement functions for 'roc' slot
scatterAccessor and replacement functions for 'scatter' slot
scoreAccessor and replacement functions for 'score' slot
splvAccessor and replacement functions for 'splv' slot
stratiflevelsAccessor function for stratification levels
svalAccessor and replacement functions for 'sval' slot
tprAccessor and replacement functions for 'tpr' slot
truthAccessor and replacement functions for 'truth' slot
update_cobradataUpdate 'COBRAData' object to the current version of the class...
update_cobraperformanceUpdate 'COBRAPerformance' or 'COBRAPlot' object to the...
iCOBRA documentation built on Nov. 17, 2017, 8:47 a.m.