# Comparison and Visualization of Ranking and Assignment Methods

## Documentation for package ‘iCOBRA’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

B C D E F M O P R S T U misc

## -- 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