actualOutcome	ClassifyResult-class
actualOutcome,ClassifyResult-method	ClassifyResult-class
allFeatureNames	ClassifyResult-class
allFeatureNames,ClassifyResult-method	ClassifyResult-class
asthma	asthma
available	available
bubblePlot.PrecisionPathways	precisionPathwaysEvaluations
calcCostsAndPerformance	precisionPathwaysEvaluations
calcCVperformance	calcPerformance
calcCVperformance,ClassifyResult-method	calcPerformance
calcExternalPerformance	calcPerformance
calcExternalPerformance,factor,factor-method	calcPerformance
calcExternalPerformance,factor,tabular-method	calcPerformance
calcExternalPerformance,Surv,numeric-method	calcPerformance
calcPerformance	calcPerformance
chosenFeatureNames	ClassifyResult-class
chosenFeatureNames,ClassifyResult-method	ClassifyResult-class
classes	asthma
ClassifyResult	ClassifyResult-class
ClassifyResult,DataFrame,character,characterOrDataFrame-method	ClassifyResult-class
ClassifyResult,DataFrame,character-method	ClassifyResult-class
ClassifyResult-class	ClassifyResult-class
clinical	METABRICclinical
colCoxTests	colCoxTests
crissCrossPlot	crissCrossPlot
crissCrossValidate	crissCrossValidate
crossValidate	crossValidate
crossValidate,data.frame-method	crossValidate
crossValidate,DataFrame-method	crossValidate
crossValidate,matrix-method	crossValidate
crossValidate,MultiAssayExperiment-method,	crossValidate
crossValidate,MultiAssayExperimentOrList-method	crossValidate
CrossValParams	CrossValParams-class
CrossValParams-class	CrossValParams-class
distribution	distribution
distribution,ClassifyResult-method	distribution
edgesToHubNetworks	edgesToHubNetworks
features	ClassifyResult-class
features,ClassifyResult-method	ClassifyResult-class
FeatureSetCollection	FeatureSetCollection
FeatureSetCollection,list-method	FeatureSetCollection
FeatureSetCollection-class	FeatureSetCollection
featureSetSummary	featureSetSummary
featureSetSummary,DataFrame-method	featureSetSummary
featureSetSummary,matrix-method	featureSetSummary
featureSetSummary,MultiAssayExperiment-method	featureSetSummary
finalModel	ClassifyResult-class
finalModel,ClassifyResult-method	ClassifyResult-class
flowchart.PrecisionPathways	precisionPathwaysEvaluations
HuRI	HuRI
interactorDifferences	interactorDifferences
interactorDifferences,DataFrame-method	interactorDifferences
interactorDifferences,matrix-method	interactorDifferences
interactorDifferences,MultiAssayExperiment-method	interactorDifferences
interactors	HuRI
length,FeatureSetCollection-method	FeatureSetCollection
measurements	asthma
METABRICclinical	METABRICclinical
ModellingParams	ModellingParams-class
ModellingParams-class	ModellingParams-class
models	ClassifyResult-class
models,ClassifyResult-method	ClassifyResult-class
performance	ClassifyResult-class
performance,ClassifyResult-method	ClassifyResult-class
performancePlot	performancePlot
performancePlot,ClassifyResult-method	performancePlot
performancePlot,list-method	performancePlot
performanceTable	calcPerformance
plotFeatureClasses	plotFeatureClasses
plotFeatureClasses,DataFrame-method	plotFeatureClasses
plotFeatureClasses,matrix-method	plotFeatureClasses
plotFeatureClasses,MultiAssayExperiment-method	plotFeatureClasses
precisionPathwaysPredict	precisionPathways
precisionPathwaysPredict,PrecisionPathways,MultiAssayExperimentOrList-method	precisionPathways
precisionPathwaysTrain	precisionPathways
precisionPathwaysTrain,MultiAssayExperimentOrList-method	precisionPathways
predict.trainedByClassifyR	crossValidate
predictions	ClassifyResult-class
predictions,ClassifyResult-method	ClassifyResult-class
PredictParams	PredictParams-class
PredictParams,characterOrFunction-method	PredictParams-class
PredictParams,missing-method	PredictParams-class
PredictParams-class	PredictParams-class
prepareData	prepareData
prepareData,data.frame-method	prepareData
prepareData,DataFrame-method	prepareData
prepareData,list-method	prepareData
prepareData,matrix-method	prepareData
prepareData,MultiAssayExperiment-method	prepareData
rankingPlot	rankingPlot
rankingPlot,ClassifyResult-method	rankingPlot
rankingPlot,list-method	rankingPlot
ROCplot	ROCplot
ROCplot,ClassifyResult-method	ROCplot
ROCplot,list-method	ROCplot
runTest	runTest
runTest,DataFrame-method	runTest
runTest,matrix-method	runTest
runTest,MultiAssayExperiment-method	runTest
runTests	runTests
runTests,DataFrame-method	runTests
runTests,matrix-method	runTests
runTests,MultiAssayExperiment-method	runTests
sampleNames	ClassifyResult-class
sampleNames,ClassifyResult-method	ClassifyResult-class
samplesMetricMap	samplesMetricMap
samplesMetricMap,ClassifyResult-method	samplesMetricMap
samplesMetricMap,list-method	samplesMetricMap
samplesMetricMap,matrix-method	samplesMetricMap
selectionPlot	selectionPlot
selectionPlot,ClassifyResult-method	selectionPlot
selectionPlot,list-method	selectionPlot
SelectParams	SelectParams-class
SelectParams,characterOrList-method	SelectParams-class
SelectParams,missing-method	SelectParams-class
SelectParams-class	SelectParams-class
show,ClassifyResult-method	ClassifyResult-class
show,FeatureSetCollection-method	FeatureSetCollection
show,PredictParams-method	PredictParams-class
show,SelectParams-method	SelectParams-class
show,TrainParams-method	TrainParams-class
show,TransformParams-method	TransformParams-class
strataPlot.PrecisionPathways	precisionPathwaysEvaluations
summary.PrecisionPathways	precisionPathwaysEvaluations
totalPredictions	ClassifyResult-class
totalPredictions,ClassifyResult-method	ClassifyResult-class
train.data.frame	crossValidate
train.DataFrame	crossValidate
train.list	crossValidate
train.matrix	crossValidate
train.MultiAssayExperiment	crossValidate
TrainParams	TrainParams-class
TrainParams,characterOrFunction-method	TrainParams-class
TrainParams,missing-method	TrainParams-class
TrainParams-class	TrainParams-class
TransformParams	TransformParams-class
TransformParams,ANY-method	TransformParams-class
TransformParams,character-method	TransformParams-class
TransformParams-class	TransformParams-class
tunedParameters	ClassifyResult-class
tunedParameters,ClassifyResult-method	ClassifyResult-class
[,FeatureSetCollection,numeric,missing,ANY-method	FeatureSetCollection
[[,FeatureSetCollection,ANY,missing-method	FeatureSetCollection
