.COBRAData	COBRAData
.COBRAPerformance	COBRAPerformance
.COBRAPlot	COBRAPlot
basemethods	basemethods
basemethods,COBRAPerformance-method	basemethods
basemethods,COBRAPlot-method	basemethods
calculate_adjp	calculate_adjp
calculate_performance	calculate_performance
COBRAapp	COBRAapp
COBRAData	COBRAData
COBRAData-class	COBRAData
cobradata_example	cobradata_example
COBRAData_from_text	COBRAData
COBRAData_to_text	COBRAData
COBRAPerformance	COBRAPerformance
COBRAPerformance-class	COBRAPerformance
COBRAPlot	COBRAPlot
COBRAPlot,COBRAPerformance-method	coerce
COBRAPlot-class	COBRAPlot
coerce	coerce
coerce,	coerce
coerce,COBRAPerformance,COBRAPlot-method	coerce
coerce,COBRAPlot,COBRAPerformance-method	coerce
corr	corr
corr,COBRAPerformance-method	corr
corr,COBRAPlot-method	corr
corr<-	corr
corr<-,COBRAPerformance,data.frame-method	corr
corr<-,COBRAPlot,data.frame-method	corr
deviation	deviation
deviation,COBRAPerformance-method	deviation
deviation,COBRAPlot-method	deviation
deviation<-	deviation
deviation<-,COBRAPerformance,data.frame-method	deviation
deviation<-,COBRAPlot,data.frame-method	deviation
Extract	Extract
facetted	facetted
facetted,COBRAPlot-method	facetted
facetted<-	facetted
facetted<-,COBRAPlot,logical-method	facetted
fdrnbr	fdrnbr
fdrnbr,COBRAPerformance-method	fdrnbr
fdrnbr,COBRAPlot-method	fdrnbr
fdrnbr<-	fdrnbr
fdrnbr<-,COBRAPerformance,data.frame-method	fdrnbr
fdrnbr<-,COBRAPlot,data.frame-method	fdrnbr
fdrnbrcurve	fdrnbrcurve
fdrnbrcurve,COBRAPerformance-method	fdrnbrcurve
fdrnbrcurve,COBRAPlot-method	fdrnbrcurve
fdrnbrcurve<-	fdrnbrcurve
fdrnbrcurve<-,COBRAPerformance,data.frame-method	fdrnbrcurve
fdrnbrcurve<-,COBRAPlot,data.frame-method	fdrnbrcurve
fdrtpr	fdrtpr
fdrtpr,COBRAPerformance-method	fdrtpr
fdrtpr,COBRAPlot-method	fdrtpr
fdrtpr<-	fdrtpr
fdrtpr<-,COBRAPerformance,data.frame-method	fdrtpr
fdrtpr<-,COBRAPlot,data.frame-method	fdrtpr
fdrtprcurve	fdrtprcurve
fdrtprcurve,COBRAPerformance-method	fdrtprcurve
fdrtprcurve,COBRAPlot-method	fdrtprcurve
fdrtprcurve<-	fdrtprcurve
fdrtprcurve<-,COBRAPerformance,data.frame-method	fdrtprcurve
fdrtprcurve<-,COBRAPlot,data.frame-method	fdrtprcurve
fpc	fpc
fpc,COBRAPerformance-method	fpc
fpc,COBRAPlot-method	fpc
fpc<-	fpc
fpc<-,COBRAPerformance,data.frame-method	fpc
fpc<-,COBRAPlot,data.frame-method	fpc
fpr	fpr
fpr,COBRAPerformance-method	fpr
fpr,COBRAPlot-method	fpr
fpr<-	fpr
fpr<-,COBRAPerformance,data.frame-method	fpr
fpr<-,COBRAPlot,data.frame-method	fpr
maxsplit	maxsplit
maxsplit,COBRAPerformance-method	maxsplit
maxsplit,COBRAPlot-method	maxsplit
maxsplit<-	maxsplit
maxsplit<-,COBRAPerformance,numeric-method	maxsplit
maxsplit<-,COBRAPlot,numeric-method	maxsplit
onlyshared	onlyshared
onlyshared,COBRAPerformance-method	onlyshared
onlyshared,COBRAPlot-method	onlyshared
onlyshared<-	onlyshared
onlyshared<-,COBRAPerformance,logical-method	onlyshared
onlyshared<-,COBRAPlot,logical-method	onlyshared
overlap	overlap
overlap,COBRAPerformance-method	overlap
overlap,COBRAPlot-method	overlap
overlap<-	overlap
overlap<-,COBRAPerformance,list_df-method	overlap
overlap<-,COBRAPlot,list_df-method	overlap
padj	padj
padj,COBRAData-method	padj
padj<-	padj
padj<-,COBRAData,data.frame-method	padj
plotcolors	plotcolors
plotcolors,COBRAPlot-method	plotcolors
plotcolors<-	plotcolors
plotcolors<-,COBRAPlot,character-method	plotcolors
plot_corr	plot_corr
plot_deviation	plot_deviation
plot_fdrnbrcurve	plot_fdrnbrcurve
plot_fdrtprcurve	plot_fdrtprcurve
plot_fpc	plot_fpc
plot_fpr	plot_fpr
plot_overlap	plot_overlap
plot_roc	plot_roc
plot_scatter	plot_scatter
plot_tpr	plot_tpr
plot_upset	plot_upset
prepare_data_for_plot	prepare_data_for_plot
pval	pval
pval,COBRAData-method	pval
pval<-	pval
pval<-,COBRAData,data.frame-method	pval
reorder_levels	reorder_levels
roc	roc
roc,COBRAPerformance-method	roc
roc,COBRAPlot-method	roc
roc<-	roc
roc<-,COBRAPerformance,data.frame-method	roc
roc<-,COBRAPlot,data.frame-method	roc
scatter	scatter
scatter,COBRAPerformance-method	scatter
scatter,COBRAPlot-method	scatter
scatter<-	scatter
scatter<-,COBRAPerformance,data.frame-method	scatter
scatter<-,COBRAPlot,data.frame-method	scatter
score	score
score,COBRAData-method	score
score<-	score
score<-,COBRAData,data.frame-method	score
splv	splv
splv,COBRAPerformance-method	splv
splv,COBRAPlot-method	splv
splv<-	splv
splv<-,COBRAPerformance,character-method	splv
splv<-,COBRAPlot,character-method	splv
stratiflevels	stratiflevels
stratiflevels,COBRAPerformance-method	stratiflevels
stratiflevels,COBRAPlot-method	stratiflevels
tpr	tpr
tpr,COBRAPerformance-method	tpr
tpr,COBRAPlot-method	tpr
tpr<-	tpr
tpr<-,COBRAPerformance,data.frame-method	tpr
tpr<-,COBRAPlot,data.frame-method	tpr
truth	truth
truth,COBRAData-method	truth
truth<-	truth
truth<-,COBRAData,data.frame-method	truth
[	Extract
[,COBRAData-method	Extract
[,COBRAPerformance-method	Extract
[,COBRAPlot-method	Extract
\S4method{[}{COBRAData,ANY,ANY,ANY}	Extract
\S4method{[}{COBRAData,ANY,ANY}	Extract
\S4method{[}{COBRAPerformance,ANY,ANY,ANY}	Extract
\S4method{[}{COBRAPerformance,ANY,ANY}	Extract
\S4method{[}{COBRAPlot,ANY,ANY,ANY}	Extract
\S4method{[}{COBRAPlot,ANY,ANY}	Extract
