Package index • iCOBRA

All functions

COBRAData() COBRAData_from_text() COBRAData_to_text(): COBRAData object and constructor
COBRAPerformance(): COBRAPerformance object and constructor
COBRAPlot(): COBRAPlot object and constructor
COBRAapp(): Interactive shiny app to visualize results
`[`(<COBRAData>) `[`(<COBRAPerformance>) `[`(<COBRAPlot>): 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 coerce,COBRAPerformance,COBRAPlot-method coerce, COBRAPlot,COBRAPerformance-method coerce,COBRAPlot,COBRAPerformance-method: Convert an object to another class
corr() `corr<-`(): Accessor and replacement functions for corr slot
deviation() `deviation<-`(): Accessor and replacement functions for deviation slot
facetted() `facetted<-`(): Accessor and replacement functions for facetted slot
fdrnbr() `fdrnbr<-`(): Accessor and replacement functions for fdrnbr slot
fdrnbrcurve() `fdrnbrcurve<-`(): Accessor and replacement functions for fdrnbrcurve slot
fdrtpr() `fdrtpr<-`(): Accessor and replacement functions for fdrtpr slot
fdrtprcurve() `fdrtprcurve<-`(): Accessor and replacement functions for fdrtprcurve slot
fpc() `fpc<-`(): Accessor and replacement functions for fpc slot
fpr() `fpr<-`(): Accessor and replacement functions for fpr slot
fsrnbr() `fsrnbr<-`(): Accessor and replacement functions for fsrnbr slot
fsrnbrcurve() `fsrnbrcurve<-`(): Accessor and replacement functions for fsrnbrcurve slot
maxsplit() `maxsplit<-`(): Accessor and replacement functions for maxsplit slot
onlyshared() `onlyshared<-`(): Accessor and replacement functions for onlyshared slot
overlap() `overlap<-`(): Accessor and replacement functions for overlap slot
padj() `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() `plotcolors<-`(): Accessor and replacement functions for plotcolors slot
prepare_data_for_plot(): Prepare data for plotting
pval() `pval<-`(): Accessor and replacement functions for pval slot
reorder_levels(): Reorder levels in COBRAPlot object
roc() `roc<-`(): Accessor and replacement functions for roc slot
scatter() `scatter<-`(): Accessor and replacement functions for scatter slot
score() `score<-`(): Accessor and replacement functions for score slot
splv() `splv<-`(): Accessor and replacement functions for splv slot
stratiflevels(): Accessor function for stratification levels
sval() `sval<-`(): Accessor and replacement functions for sval slot
tpr() `tpr<-`(): Accessor and replacement functions for tpr slot
truth() `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