actualClasses	ClassifyResult-class
actualClasses,ClassifyResult-method	ClassifyResult-class
bartlettSelection	bartlettSelection
bartlettSelection,DataFrame-method	bartlettSelection
bartlettSelection,matrix-method	bartlettSelection
bartlettSelection,MultiAssayExperiment-method	bartlettSelection
calcCVperformance	calcPerformance
calcCVperformance,ClassifyResult-method	calcPerformance
calcExternalPerformance	calcPerformance
calcExternalPerformance,factor,factor-method	calcPerformance
calcPerformance	calcPerformance
characterOrDataFrame	characterOrDataFrame-class
characterOrDataFrame-class	characterOrDataFrame-class
classes	asthmaDataset
classifyInterface	classifyInterface
classifyInterface,DataFrame-method	classifyInterface
classifyInterface,matrix-method	classifyInterface
classifyInterface,MultiAssayExperiment-method	classifyInterface
ClassifyResult	ClassifyResult-class
ClassifyResult,character,character,character,character,character-method	ClassifyResult-class
ClassifyResult-class	ClassifyResult-class
differentMeansSelection	differentMeansSelection
differentMeansSelection,DataFrame-method	differentMeansSelection
differentMeansSelection,matrix-method	differentMeansSelection
differentMeansSelection,MultiAssayExperiment-method	differentMeansSelection
distribution	distribution
distribution,ClassifyResult-method	distribution
dlda	dlda-class
dlda-class	dlda-class
DLDApredictInterface	DLDAinterface
DLDApredictInterface,dlda,DataFrame-method	DLDAinterface
DLDApredictInterface,dlda,matrix-method	DLDAinterface
DLDApredictInterface,dlda,MultiAssayExperiment-method	DLDAinterface
DLDAtrainInterface	DLDAinterface
DLDAtrainInterface,DataFrame-method	DLDAinterface
DLDAtrainInterface,matrix-method	DLDAinterface
DLDAtrainInterface,MultiAssayExperiment-method	DLDAinterface
DMDselection	DMDselection
DMDselection,DataFrame-method	DMDselection
DMDselection,matrix-method	DMDselection
DMDselection,MultiAssayExperiment-method	DMDselection
edgeRselection	edgeRselection
edgeRselection,DataFrame-method	edgeRselection
edgeRselection,matrix-method	edgeRselection
edgeRselection,MultiAssayExperiment-method	edgeRselection
edgesToHubNetworks	edgesToHubNetworks
elasticNetFeatures	elasticNetFeatures
elasticNetFeatures,multnet-method	elasticNetFeatures
elasticNetGLMinterface	elasticNetGLMinterface
elasticNetGLMpredictInterface	elasticNetGLMinterface
elasticNetGLMpredictInterface,multnet,DataFrame-method	elasticNetGLMinterface
elasticNetGLMpredictInterface,multnet,matrix-method	elasticNetGLMinterface
elasticNetGLMpredictInterface,multnet,MultiAssayExperiment-method	elasticNetGLMinterface
elasticNetGLMtrainInterface	elasticNetGLMinterface
elasticNetGLMtrainInterface,DataFrame-method	elasticNetGLMinterface
elasticNetGLMtrainInterface,matrix-method	elasticNetGLMinterface
elasticNetGLMtrainInterface,MultiAssayExperiment-method	elasticNetGLMinterface
featureNames	ClassifyResult-class
featureNames,ClassifyResult-method	ClassifyResult-class
features	ClassifyResult-class
features,ClassifyResult-method	ClassifyResult-class
FeatureSetCollection	FeatureSetCollection-class
FeatureSetCollection,list-method	FeatureSetCollection-class
FeatureSetCollection-class	FeatureSetCollection-class
FeatureSetCollectionOrNULL	FeatureSetCollectionOrNULL-class
FeatureSetCollectionOrNULL-class	FeatureSetCollectionOrNULL-class
featureSetSummary	featureSetSummary
featureSetSummary,DataFrame-method	featureSetSummary
featureSetSummary,matrix-method	featureSetSummary
featureSetSummary,MultiAssayExperiment-method	featureSetSummary
fisherDiscriminant	fisherDiscriminant
fisherDiscriminant,DataFrame-method	fisherDiscriminant
fisherDiscriminant,matrix-method	fisherDiscriminant
fisherDiscriminant,MultiAssayExperiment-method	fisherDiscriminant
forestFeatures	forestFeatures
forestFeatures,randomForest-method	forestFeatures
functionOrList	functionOrList-class
functionOrList-class	functionOrList-class
functionOrNULL	functionOrNULL-class
functionOrNULL-class	functionOrNULL-class
getLocationsAndScales	getLocationsAndScales
getLocationsAndScales,DataFrame-method	getLocationsAndScales
getLocationsAndScales,matrix-method	getLocationsAndScales
getLocationsAndScales,MultiAssayExperiment-method	getLocationsAndScales
integerOrNumeric	integerOrNumeric-class
integerOrNumeric-class	integerOrNumeric-class
interactorDifferences	interactorDifferences
interactorDifferences,DataFrame-method	interactorDifferences
interactorDifferences,matrix-method	interactorDifferences
interactorDifferences,MultiAssayExperiment-method	interactorDifferences
kNNinterface	knnInterface
kNNinterface,DataFrame-method	knnInterface
kNNinterface,matrix-method	knnInterface
kNNinterface,MultiAssayExperiment-method	knnInterface
KolmogorovSmirnovSelection	KolmogorovSmirnovSelection
KolmogorovSmirnovSelection,DataFrame-method	KolmogorovSmirnovSelection
KolmogorovSmirnovSelection,matrix-method	KolmogorovSmirnovSelection
KolmogorovSmirnovSelection,MultiAssayExperiment-method	KolmogorovSmirnovSelection
kTSPclassifier	kTSPclassifier
kTSPclassifier,DataFrame-method	kTSPclassifier
kTSPclassifier,matrix-method	kTSPclassifier
kTSPclassifier,MultiAssayExperiment-method	kTSPclassifier
KullbackLeiblerSelection	KullbackLeiblerSelection
KullbackLeiblerSelection,DataFrame-method	KullbackLeiblerSelection
KullbackLeiblerSelection,matrix-method	KullbackLeiblerSelection
KullbackLeiblerSelection,MultiAssayExperiment-method	KullbackLeiblerSelection
length,FeatureSetCollection-method	FeatureSetCollection-class
leveneSelection	leveneSelection
leveneSelection,DataFrame-method	leveneSelection
leveneSelection,matrix-method	leveneSelection
leveneSelection,MultiAssayExperiment-method	leveneSelection
likelihoodRatioSelection	likelihoodRatioSelection
likelihoodRatioSelection,DataFrame-method	likelihoodRatioSelection
likelihoodRatioSelection,matrix-method	likelihoodRatioSelection
likelihoodRatioSelection,MultiAssayExperiment-method	likelihoodRatioSelection
limmaSelection	limmaSelection
limmaSelection,DataFrame-method	limmaSelection
limmaSelection,matrix-method	limmaSelection
limmaSelection,MultiAssayExperiment-method	limmaSelection
measurements	asthmaDataset
mixmodels	mixmodels
mixModelsPredict	mixmodels
mixModelsPredict,list,DataFrame-method	mixmodels
mixModelsPredict,list,matrix-method	mixmodels
mixModelsPredict,list,MultiAssayExperiment-method	mixmodels
mixModelsTrain	mixmodels
mixModelsTrain,DataFrame-method	mixmodels
mixModelsTrain,matrix-method	mixmodels
mixModelsTrain,MultiAssayExperiment-method	mixmodels
models	ClassifyResult-class
models,ClassifyResult-method	ClassifyResult-class
multnet	multnet-class
multnet-class	multnet-class
naiveBayesKernel	naiveBayesKernel
naiveBayesKernel,DataFrame-method	naiveBayesKernel
naiveBayesKernel,matrix-method	naiveBayesKernel
naiveBayesKernel,MultiAssayExperiment-method	naiveBayesKernel
networkCorrelationsSelection	networkCorrelationsSelection
networkCorrelationsSelection,DataFrame-method	networkCorrelationsSelection
networkCorrelationsSelection,matrix-method	networkCorrelationsSelection
networkCorrelationsSelection,MultiAssayExperiment-method	networkCorrelationsSelection
NSCpredictInterface	NSCpredictInterface
NSCpredictInterface,pamrtrained,DataFrame-method	NSCpredictInterface
NSCpredictInterface,pamrtrained,matrix-method	NSCpredictInterface
NSCpredictInterface,pamrtrained,MultiAssayExperiment-method	NSCpredictInterface
NSCselectionInterface	NSCselectionInterface
NSCselectionInterface,DataFrame-method	NSCselectionInterface
NSCselectionInterface,matrix-method	NSCselectionInterface
NSCselectionInterface,MultiAssayExperiment-method	NSCselectionInterface
NSCtrainInterface	NSCtrainInterface
NSCtrainInterface,DataFrame-method	NSCtrainInterface
NSCtrainInterface,matrix-method	NSCtrainInterface
NSCtrainInterface,MultiAssayExperiment-method	NSCtrainInterface
pairsDifferencesSelection	pairsDifferencesSelection
pairsDifferencesSelection,DataFrame-method	pairsDifferencesSelection
pairsDifferencesSelection,matrix-method	pairsDifferencesSelection
pairsDifferencesSelection,MultiAssayExperiment-method	pairsDifferencesSelection
pamrtrained	pamrtrained-class
pamrtrained-class	pamrtrained-class
performance	ClassifyResult-class
performance,ClassifyResult-method	ClassifyResult-class
performancePlot	performancePlot
performancePlot,list-method	performancePlot
plotFeatureClasses	plotFeatureClasses
plotFeatureClasses,DataFrame-method	plotFeatureClasses
plotFeatureClasses,matrix-method	plotFeatureClasses
plotFeatureClasses,MultiAssayExperiment-method	plotFeatureClasses
predictions	ClassifyResult-class
predictions,ClassifyResult-method	ClassifyResult-class
PredictParams	PredictParams-class
PredictParams,ANY-method	PredictParams-class
PredictParams,functionOrNULL-method	PredictParams-class
PredictParams-class	PredictParams-class
previousSelection	previousSelection
previousSelection,DataFrame-method	previousSelection
previousSelection,matrix-method	previousSelection
previousSelection,MultiAssayExperiment-method	previousSelection
previousTrained	previousTrained
previousTrained,ClassifyResult-method	previousTrained
randomForest	randomForest-class
randomForest-class	randomForest-class
randomForestInterface	randomForestInterface
randomForestPredictInterface	randomForestInterface
randomForestPredictInterface,randomForest,DataFrame-method	randomForestInterface
randomForestPredictInterface,randomForest,matrix-method	randomForestInterface
randomForestPredictInterface,randomForest,MultiAssayExperiment-method	randomForestInterface
randomForestTrainInterface	randomForestInterface
randomForestTrainInterface,DataFrame-method	randomForestInterface
randomForestTrainInterface,matrix-method	randomForestInterface
randomForestTrainInterface,MultiAssayExperiment-method	randomForestInterface
rankingPlot	rankingPlot
rankingPlot,list-method	rankingPlot
ResubstituteParams	ResubstituteParams-class
ResubstituteParams,ANY,ANY,ANY-method	ResubstituteParams-class
ResubstituteParams,numeric,character,character-method	ResubstituteParams-class
ResubstituteParams-class	ResubstituteParams-class
ROCplot	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,list-method	samplesMetricMap
samplesMetricMap,matrix-method	samplesMetricMap
selectionPlot	selectionPlot
selectionPlot,list-method	selectionPlot
SelectParams	SelectParams-class
SelectParams,ANY-method	SelectParams-class
SelectParams,functionOrList-method	SelectParams-class
SelectParams-class	SelectParams-class
SelectResult	SelectResult-class
SelectResult,character,character,numeric,list,list-method	SelectResult-class
SelectResult-class	SelectResult-class
show,ClassifyResult-method	ClassifyResult-class
show,FeatureSetCollection-method	FeatureSetCollection-class
show,SelectResult-method	SelectResult-class
subtractFromLocation	subtractFromLocation
subtractFromLocation,DataFrame-method	subtractFromLocation
subtractFromLocation,matrix-method	subtractFromLocation
subtractFromLocation,MultiAssayExperiment-method	subtractFromLocation
svm	svm-class
svm-class	svm-class
SVMpredictInterface	SVMinterface
SVMpredictInterface,svm,DataFrame-method	SVMinterface
SVMpredictInterface,svm,matrix-method	SVMinterface
SVMpredictInterface,svm,MultiAssayExperiment-method	SVMinterface
SVMtrainInterface	SVMinterface
SVMtrainInterface,DataFrame-method	SVMinterface
SVMtrainInterface,matrix-method	SVMinterface
SVMtrainInterface,MultiAssayExperiment-method	SVMinterface
totalPredictions	ClassifyResult-class
totalPredictions,ClassifyResult-method	ClassifyResult-class
TrainParams	TrainParams-class
TrainParams,ANY-method	TrainParams-class
TrainParams,function-method	TrainParams-class
TrainParams-class	TrainParams-class
TransformParams	TransformParams-class
TransformParams,ANY-method	TransformParams-class
TransformParams,function-method	TransformParams-class
TransformParams-class	TransformParams-class
tunedParameters	ClassifyResult-class
tunedParameters,ClassifyResult-method	ClassifyResult-class
[,FeatureSetCollection,integerOrNumeric,missing,ANY-method	FeatureSetCollection-class
[[,FeatureSetCollection,ANY,missing-method	FeatureSetCollection-class
