actualOutcomes	ClassifyResult-class
actualOutcomes,ClassifyResult-method	ClassifyResult-class
allFeatureNames	ClassifyResult-class
allFeatureNames,ClassifyResult-method	ClassifyResult-class
asthma	asthma
bartlettRanking	bartlettRanking
bartlettRanking,DataFrame-method	bartlettRanking
bartlettRanking,matrix-method	bartlettRanking
bartlettRanking,MultiAssayExperiment-method	bartlettRanking
calcCVperformance	calcPerformance
calcCVperformance,ClassifyResult-method	calcPerformance
calcExternalPerformance	calcPerformance
calcExternalPerformance,factor,factor-method	calcPerformance
calcExternalPerformance,Surv,numeric-method	calcPerformance
calcPerformance	calcPerformance
characterOrDataFrame	characterOrDataFrame-class
characterOrDataFrame-class	characterOrDataFrame-class
chosenFeatureNames	ClassifyResult-class
chosenFeatureNames,ClassifyResult-method	ClassifyResult-class
classes	asthma
classifyInterface	classifyInterface
classifyInterface,DataFrame-method	classifyInterface
classifyInterface,matrix-method	classifyInterface
classifyInterface,MultiAssayExperiment-method	classifyInterface
ClassifyResult	ClassifyResult-class
ClassifyResult,DataFrame,character,characterOrDataFrame-method	ClassifyResult-class
ClassifyResult-class	ClassifyResult-class
coxnetInterface	coxnetInterface
coxnetPredictInterface	coxnetInterface
coxnetPredictInterface,coxnet,DataFrame-method	coxnetInterface
coxnetPredictInterface,coxnet,matrix-method	coxnetInterface
coxnetPredictInterface,coxnet,MultiAssayExperiment-method	coxnetInterface
coxnetPredictInterface,multnet,DataFrame-method	coxnetInterface
coxnetPredictInterface,multnet,matrix-method	coxnetInterface
coxnetPredictInterface,multnet,MultiAssayExperiment-method	coxnetInterface
coxnetTrainInterface	coxnetInterface
coxnetTrainInterface,DataFrame-method	coxnetInterface
coxnetTrainInterface,matrix-method	coxnetInterface
coxnetTrainInterface,MultiAssayExperiment-method	coxnetInterface
coxph	coxph-class
coxph-class	coxph-class
coxphInterface	coxphInterface
coxphInterface,DataFrame-method	coxphInterface
coxphInterface,matrix-method	coxphInterface
coxphInterface,MultiAssayExperiment-method	coxphInterface
coxphPredictInterface	coxphInterface
coxphPredictInterface,coxph,DataFrame-method	coxphInterface
coxphPredictInterface,coxph,matrix-method	coxphInterface
coxphPredictInterface,coxph,MultiAssayExperiment-method	coxphInterface
coxphRanking	coxphRanking
coxphRanking,DataFrame-method	coxphRanking
coxphRanking,matrix-method	coxphRanking
coxphRanking,MultiAssayExperiment-method	coxphRanking
coxphTrainInterface	coxphInterface
coxphTrainInterface,DataFrame-method	coxphInterface
coxphTrainInterface,matrix-method	coxphInterface
coxphTrainInterface,MultiAssayExperiment-method	coxphInterface
crossValidate	crossValidate
crossValidate,data.frame-method	crossValidate
crossValidate,DataFrame-method	crossValidate
crossValidate,list-method	crossValidate
crossValidate,matrix-method	crossValidate
crossValidate,MultiAssayExperiment-method	crossValidate
crossValidate,MultiAssayExperiment-method,	crossValidate
CrossValParams	CrossValParams-class
CrossValParams-class	CrossValParams-class
DataFrameOrNULL	DataFrameOrNULL-class
DataFrameOrNULL-class	DataFrameOrNULL-class
differentMeansRanking	differentMeansRanking
differentMeansRanking,DataFrame-method	differentMeansRanking
differentMeansRanking,matrix-method	differentMeansRanking
differentMeansRanking,MultiAssayExperiment-method	differentMeansRanking
distribution	distribution
distribution,ClassifyResult-method	distribution
dlda	dlda-class
DLDA Interface	DLDAinterface
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
DMDranking	DMDranking
DMDranking,DataFrame-method	DMDranking
DMDranking,matrix-method	DMDranking
DMDranking,MultiAssayExperiment-method	DMDranking
edgeRranking	edgeRranking
edgeRranking,DataFrame-method	edgeRranking
edgeRranking,matrix-method	edgeRranking
edgeRranking,MultiAssayExperiment-method	edgeRranking
edgesToHubNetworks	edgesToHubNetworks
elasticNetFeatures	elasticNetFeatures
elasticNetFeatures,multnet-method	elasticNetFeatures
elasticNetGLMinterface	elasticNetGLM
elasticNetGLMpredictInterface	elasticNetGLM
elasticNetGLMpredictInterface,multnet,DataFrame-method	elasticNetGLM
elasticNetGLMpredictInterface,multnet,matrix-method	elasticNetGLM
elasticNetGLMpredictInterface,multnet,MultiAssayExperiment-method	elasticNetGLM
elasticNetGLMtrainInterface	elasticNetGLM
elasticNetGLMtrainInterface,DataFrame-method	elasticNetGLM
elasticNetGLMtrainInterface,matrix-method	elasticNetGLM
elasticNetGLMtrainInterface,MultiAssayExperiment-method	elasticNetGLM
features	ClassifyResult-class
features,ClassifyResult-method	ClassifyResult-class
FeatureSetCollection	FeatureSetCollection
FeatureSetCollection,list-method	FeatureSetCollection
FeatureSetCollection-class	FeatureSetCollection
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
generateCrossValParams	generateCrossValParams
generateModellingParams	generateModellingParams
getLocationsAndScales	getLocationsAndScales
getLocationsAndScales,DataFrame-method	getLocationsAndScales
getLocationsAndScales,matrix-method	getLocationsAndScales
getLocationsAndScales,MultiAssayExperiment-method	getLocationsAndScales
HuRI	HuRI
interactorDifferences	interactorDifferences
interactorDifferences,DataFrame-method	interactorDifferences
interactorDifferences,matrix-method	interactorDifferences
interactorDifferences,MultiAssayExperiment-method	interactorDifferences
interactors	HuRI
kNNinterface	kNNinterface
kNNinterface,DataFrame-method	kNNinterface
kNNinterface,matrix-method	kNNinterface
kNNinterface,MultiAssayExperiment-method	kNNinterface
KolmogorovSmirnovRanking	KolmogorovSmirnovRanking
KolmogorovSmirnovRanking,DataFrame-method	KolmogorovSmirnovRanking
KolmogorovSmirnovRanking,matrix-method	KolmogorovSmirnovRanking
KolmogorovSmirnovRanking,MultiAssayExperiment-method	KolmogorovSmirnovRanking
kTSPclassifier	kTSPclassifier
kTSPclassifier,DataFrame-method	kTSPclassifier
kTSPclassifier,matrix-method	kTSPclassifier
kTSPclassifier,MultiAssayExperiment-method	kTSPclassifier
KullbackLeiblerRanking	KullbackLeiblerRanking
KullbackLeiblerRanking,DataFrame-method	KullbackLeiblerRanking
KullbackLeiblerRanking,matrix-method	KullbackLeiblerRanking
KullbackLeiblerRanking,MultiAssayExperiment-method	KullbackLeiblerRanking
length,FeatureSetCollection-method	FeatureSetCollection
leveneRanking	leveneRanking
leveneRanking,DataFrame-method	leveneRanking
leveneRanking,matrix-method	leveneRanking
leveneRanking,MultiAssayExperiment-method	leveneRanking
likelihoodRatioRanking	likelihoodRatioRanking
likelihoodRatioRanking,DataFrame-method	likelihoodRatioRanking
likelihoodRatioRanking,matrix-method	likelihoodRatioRanking
likelihoodRatioRanking,MultiAssayExperiment-method	likelihoodRatioRanking
limmaRanking	limmaRanking
limmaRanking,DataFrame-method	limmaRanking
limmaRanking,matrix-method	limmaRanking
limmaRanking,MultiAssayExperiment-method	limmaRanking
listOrNULL	listOrNULL-class
listOrNULL-class	listOrNULL-class
measurements	asthma
mixmodels	mixModels
mixModelsPredict	mixModels
mixModelsPredict,MixModelsListsSet,DataFrame-method	mixModels
mixModelsPredict,MixModelsListsSet,matrix-method	mixModels
mixModelsPredict,MixModelsListsSet,MultiAssayExperiment-method	mixModels
mixModelsTrain	mixModels
mixModelsTrain,DataFrame-method	mixModels
mixModelsTrain,matrix-method	mixModels
mixModelsTrain,MultiAssayExperiment-method	mixModels
ModellingParams	ModellingParams-class
ModellingParams-class	ModellingParams-class
ModellingParamsOrNULL	ModellingParamsOrNULL-class
ModellingParamsOrNULL-class	ModellingParamsOrNULL-class
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
NSCfeatures	NSCinterface
NSCfeatures,pamrtrained-method	NSCinterface
NSCpredictInterface	NSCinterface
NSCpredictInterface,pamrtrained,DataFrame-method	NSCinterface
NSCpredictInterface,pamrtrained,matrix-method	NSCinterface
NSCpredictInterface,pamrtrained,MultiAssayExperiment-method	NSCinterface
NSCtrainInterface	NSCinterface
NSCtrainInterface,DataFrame-method	NSCinterface
NSCtrainInterface,matrix-method	NSCinterface
NSCtrainInterface,MultiAssayExperiment-method	NSCinterface
numericOrNULL	numericOrNULL-class
numericOrNULL-class	numericOrNULL-class
pairsDifferencesRanking	pairsDifferencesRanking
pairsDifferencesRanking,DataFrame-method	pairsDifferencesRanking
pairsDifferencesRanking,matrix-method	pairsDifferencesRanking
pairsDifferencesRanking,MultiAssayExperiment-method	pairsDifferencesRanking
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
predict,ClassifyResult-method	crossValidate
predictions	ClassifyResult-class
predictions,ClassifyResult-method	ClassifyResult-class
PredictParams	PredictParams-class
PredictParams,functionOrNULL-method	PredictParams-class
PredictParams,missing-method	PredictParams-class
PredictParams-class	PredictParams-class
PredictParamsOrNULL	PredictParamsOrNULL
PredictParamsOrNULL-class	PredictParamsOrNULL
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
randomForestInterfaces	randomForest
randomForestPredictInterface	randomForest
randomForestPredictInterface,randomForest,DataFrame-method	randomForest
randomForestPredictInterface,randomForest,matrix-method	randomForest
randomForestPredictInterface,randomForest,MultiAssayExperiment-method	randomForest
randomForestTrainInterface	randomForest
randomForestTrainInterface,DataFrame-method	randomForest
randomForestTrainInterface,matrix-method	randomForest
randomForestTrainInterface,MultiAssayExperiment-method	randomForest
rankingPlot	rankingPlot
rankingPlot,list-method	rankingPlot
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,functionOrList-method	SelectParams-class
SelectParams,missing-method	SelectParams-class
SelectParams-class	SelectParams-class
SelectParamsOrNULL	SelectParamsOrNULL-class
SelectParamsOrNULL-class	SelectParamsOrNULL-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
StageParams	StageParams-class
StageParams-class	StageParams-class
StageParamsOrMissing	StageParamsOrElse
StageParamsOrMissing-class	StageParamsOrElse
StageParamsOrMissingOrNULL	StageParamsOrElse
StageParamsOrMissingOrNULL-class	StageParamsOrElse
subtractFromLocation	subtractFromLocation
subtractFromLocation,DataFrame,DataFrame-method	subtractFromLocation
subtractFromLocation,matrix,matrix-method	subtractFromLocation
subtractFromLocation,MultiAssayExperiment,MultiAssayExperiment-method	subtractFromLocation
Surv	Surv-class
Surv-class	Surv-class
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,function-method	TrainParams-class
TrainParams,missing-method	TrainParams-class
TrainParams-class	TrainParams-class
TransformParams	TransformParams-class
TransformParams,ANY-method	TransformParams-class
TransformParams,function-method	TransformParams-class
TransformParams-class	TransformParams-class
TransformParamsOrNULL	TransformParamsOrNULL-class
TransformParamsOrNULL-class	TransformParamsOrNULL-class
tunedParameters	ClassifyResult-class
tunedParameters,ClassifyResult-method	ClassifyResult-class
[,FeatureSetCollection,numeric,missing,ANY-method	FeatureSetCollection
[[,FeatureSetCollection,ANY,missing-method	FeatureSetCollection
