Comparison and Visualization of Ranking and Assignment Methods
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Documentation for package ‘iCOBRA’ version 1.22.1
Help Pages
-- B --
| basemethods | Accessor function for basemethods |
| basemethods-method | Accessor function for basemethods |
-- C --
| calculate_adjp | Calculate adjusted p-values |
| calculate_performance | Calculate performance measures |
| COBRAapp | Interactive shiny app to visualize results |
| COBRAData | 'COBRAData' object and constructor |
| COBRAData-class | 'COBRAData' object and constructor |
| cobradata_example | Example data set with three differential gene expression methods |
| cobradata_example_sval | Example data set with three differential gene expression methods |
| COBRAData_from_text | 'COBRAData' object and constructor |
| COBRAData_to_text | 'COBRAData' object and constructor |
| COBRAPerformance | 'COBRAPerformance' object and constructor |
| COBRAPerformance-class | 'COBRAPerformance' object and constructor |
| COBRAPlot | 'COBRAPlot' object and constructor |
| COBRAPlot-class | 'COBRAPlot' object and constructor |
| COBRAPlot-method | Convert an object to another class |
| coerce | Convert an object to another class |
| coerce, | Convert an object to another class |
| coerce-method | Convert an object to another class |
| corr | Accessor and replacement functions for 'corr' slot |
| corr-method | Accessor and replacement functions for 'corr' slot |
| corr<- | Accessor and replacement functions for 'corr' slot |
| corr<--method | Accessor and replacement functions for 'corr' slot |
-- D --
| deviation | Accessor and replacement functions for 'deviation' slot |
| deviation-method | Accessor and replacement functions for 'deviation' slot |
| deviation<- | Accessor and replacement functions for 'deviation' slot |
| deviation<--method | Accessor and replacement functions for 'deviation' slot |
-- E --
| Extract | Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot' objects |
-- F --
| facetted | Accessor and replacement functions for 'facetted' slot |
| facetted-method | Accessor and replacement functions for 'facetted' slot |
| facetted<- | Accessor and replacement functions for 'facetted' slot |
| facetted<--method | Accessor and replacement functions for 'facetted' slot |
| fdrnbr | Accessor and replacement functions for 'fdrnbr' slot |
| fdrnbr-method | Accessor and replacement functions for 'fdrnbr' slot |
| fdrnbr<- | Accessor and replacement functions for 'fdrnbr' slot |
| fdrnbr<--method | Accessor and replacement functions for 'fdrnbr' slot |
| fdrnbrcurve | Accessor and replacement functions for 'fdrnbrcurve' slot |
| fdrnbrcurve-method | Accessor and replacement functions for 'fdrnbrcurve' slot |
| fdrnbrcurve<- | Accessor and replacement functions for 'fdrnbrcurve' slot |
| fdrnbrcurve<--method | Accessor and replacement functions for 'fdrnbrcurve' slot |
| fdrtpr | Accessor and replacement functions for 'fdrtpr' slot |
| fdrtpr-method | Accessor and replacement functions for 'fdrtpr' slot |
| fdrtpr<- | Accessor and replacement functions for 'fdrtpr' slot |
| fdrtpr<--method | Accessor and replacement functions for 'fdrtpr' slot |
| fdrtprcurve | Accessor and replacement functions for 'fdrtprcurve' slot |
| fdrtprcurve-method | Accessor and replacement functions for 'fdrtprcurve' slot |
| fdrtprcurve<- | Accessor and replacement functions for 'fdrtprcurve' slot |
| fdrtprcurve<--method | Accessor and replacement functions for 'fdrtprcurve' slot |
| fpc | Accessor and replacement functions for 'fpc' slot |
| fpc-method | Accessor and replacement functions for 'fpc' slot |
| fpc<- | Accessor and replacement functions for 'fpc' slot |
| fpc<--method | Accessor and replacement functions for 'fpc' slot |
| fpr | Accessor and replacement functions for 'fpr' slot |
| fpr-method | Accessor and replacement functions for 'fpr' slot |
| fpr<- | Accessor and replacement functions for 'fpr' slot |
| fpr<--method | Accessor and replacement functions for 'fpr' slot |
| fsrnbr | Accessor and replacement functions for 'fsrnbr' slot |
| fsrnbr-method | Accessor and replacement functions for 'fsrnbr' slot |
| fsrnbr<- | Accessor and replacement functions for 'fsrnbr' slot |
| fsrnbr<--method | Accessor and replacement functions for 'fsrnbr' slot |
| fsrnbrcurve | Accessor and replacement functions for 'fsrnbrcurve' slot |
| fsrnbrcurve-method | Accessor and replacement functions for 'fsrnbrcurve' slot |
| fsrnbrcurve<- | Accessor and replacement functions for 'fsrnbrcurve' slot |
| fsrnbrcurve<--method | Accessor and replacement functions for 'fsrnbrcurve' slot |
-- M --
| maxsplit | Accessor and replacement functions for 'maxsplit' slot |
| maxsplit-method | Accessor and replacement functions for 'maxsplit' slot |
| maxsplit<- | Accessor and replacement functions for 'maxsplit' slot |
| maxsplit<--method | Accessor and replacement functions for 'maxsplit' slot |
-- O --
| onlyshared | Accessor and replacement functions for 'onlyshared' slot |
| onlyshared-method | Accessor and replacement functions for 'onlyshared' slot |
| onlyshared<- | Accessor and replacement functions for 'onlyshared' slot |
| onlyshared<--method | Accessor and replacement functions for 'onlyshared' slot |
| overlap | Accessor and replacement functions for 'overlap' slot |
| overlap-method | Accessor and replacement functions for 'overlap' slot |
| overlap<- | Accessor and replacement functions for 'overlap' slot |
| overlap<--method | Accessor and replacement functions for 'overlap' slot |
-- P --
| padj | Accessor and replacement functions for 'padj' slot |
| padj-method | Accessor and replacement functions for 'padj' slot |
| padj<- | Accessor and replacement functions for 'padj' slot |
| padj<--method | Accessor and replacement functions for 'padj' slot |
| plotcolors | Accessor and replacement functions for 'plotcolors' slot |
| plotcolors-method | Accessor and replacement functions for 'plotcolors' slot |
| plotcolors<- | Accessor and replacement functions for 'plotcolors' slot |
| plotcolors<--method | 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 |
| pval-method | Accessor and replacement functions for 'pval' slot |
| pval<- | Accessor and replacement functions for 'pval' slot |
| pval<--method | Accessor and replacement functions for 'pval' slot |
-- R --
| reorder_levels | Reorder levels in COBRAPlot object |
| roc | Accessor and replacement functions for 'roc' slot |
| roc-method | Accessor and replacement functions for 'roc' slot |
| roc<- | Accessor and replacement functions for 'roc' slot |
| roc<--method | Accessor and replacement functions for 'roc' slot |
-- S --
| scatter | Accessor and replacement functions for 'scatter' slot |
| scatter-method | Accessor and replacement functions for 'scatter' slot |
| scatter<- | Accessor and replacement functions for 'scatter' slot |
| scatter<--method | Accessor and replacement functions for 'scatter' slot |
| score | Accessor and replacement functions for 'score' slot |
| score-method | Accessor and replacement functions for 'score' slot |
| score<- | Accessor and replacement functions for 'score' slot |
| score<--method | Accessor and replacement functions for 'score' slot |
| splv | Accessor and replacement functions for 'splv' slot |
| splv-method | Accessor and replacement functions for 'splv' slot |
| splv<- | Accessor and replacement functions for 'splv' slot |
| splv<--method | Accessor and replacement functions for 'splv' slot |
| stratiflevels | Accessor function for stratification levels |
| stratiflevels-method | Accessor function for stratification levels |
| sval | Accessor and replacement functions for 'sval' slot |
| sval-method | Accessor and replacement functions for 'sval' slot |
| sval<- | Accessor and replacement functions for 'sval' slot |
| sval<--method | Accessor and replacement functions for 'sval' slot |
-- T --
| tpr | Accessor and replacement functions for 'tpr' slot |
| tpr-method | Accessor and replacement functions for 'tpr' slot |
| tpr<- | Accessor and replacement functions for 'tpr' slot |
| tpr<--method | Accessor and replacement functions for 'tpr' slot |
| truth | Accessor and replacement functions for 'truth' slot |
| truth-method | Accessor and replacement functions for 'truth' slot |
| truth<- | Accessor and replacement functions for 'truth' slot |
| truth<--method | Accessor and replacement functions for 'truth' slot |
-- U --
| 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 |
-- misc --
| .COBRAData | 'COBRAData' object and constructor |
| .COBRAPerformance | 'COBRAPerformance' object and constructor |
| .COBRAPlot | 'COBRAPlot' object and constructor |
| [ | Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot' objects |
| [-method | Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot' objects |
| \S4method{[}{COBRAData,ANY,ANY,ANY} | Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot' objects |
| \S4method{[}{COBRAData,ANY,ANY} | Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot' objects |
| \S4method{[}{COBRAPerformance,ANY,ANY,ANY} | Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot' objects |
| \S4method{[}{COBRAPerformance,ANY,ANY} | Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot' objects |
| \S4method{[}{COBRAPlot,ANY,ANY,ANY} | Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot' objects |
| \S4method{[}{COBRAPlot,ANY,ANY} | Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot' objects |