%*%,dgRMatrix,numeric-method	ExplicitRepresentationAccessors
%*%,matrix,dgRMatrix-method	ExplicitRepresentationAccessors
AAVector	BioVector
AAVector-class	BioVector-class
annotationCharset	annotationSpecificKernel
annotationCharset,BioVector-method	annotationSpecificKernel
annotationCharset,XStringSet-method	annotationSpecificKernel
annotationMetadata	annotationSpecificKernel
annotationMetadata,BioVector-method	annotationSpecificKernel
annotationMetadata,XStringSet-method	annotationSpecificKernel
annotationMetadata<-	annotationSpecificKernel
annotationMetadata<-,BioVector-method	annotationSpecificKernel
annotationMetadata<-,XStringSet-method	annotationSpecificKernel
AnnotationSpecificKernel	annotationSpecificKernel
annotationSpecificKernel	annotationSpecificKernel
as.character,BioVector-method	BioVector
as.KernelMatrix	KernelMatrixAccessors
as.KernelMatrix,matrix-method	KernelMatrixAccessors
auc	ROCDataAccessors
auc,ROCData-method	ROCDataAccessors
auc<-	ROCDataAccessors
auc<-,ROCData-method	ROCDataAccessors
baselines	PredictionProfileAccessors
baselines,PredictionProfile-method	PredictionProfileAccessors
BioVector	BioVector
BioVector-class	BioVector-class
c,BioVector-method	BioVector
ccannot	kebabsData
ccgroups	kebabsData
ccseq	kebabsData
character	annotationSpecificKernel
class:AAVector	BioVector-class
class:BioVector	BioVector-class
class:ControlInformation	ControlInformation-class
class:CrossValidationResult	CrossValidationResult-class
class:DNAVector	BioVector-class
class:ExplicitRepresentation	ExplicitRepresentation-class
class:ExplicitRepresentationDense	ExplicitRepresentation-class
class:ExplicitRepresentationSparse	ExplicitRepresentation-class
class:GappyPairKernel	GappyPairKernel-class
class:KBModel	KBModel-class
class:KernelMatrix	KernelMatrix-class
class:MismatchKernel	MismatchKernel-class
class:ModelSelectionResult	ModelSelectionResult-class
class:MotifKernel	MotifKernel-class
class:PredictionProfile	PredictionProfile-class
class:RNAVector	BioVector-class
class:ROCData	ROCData-class
class:SequenceKernel	SequenceKernel-class
class:SpectrumKernel	SpectrumKernel-class
class:SVMInformation	SVMInformation-class
class:SymmetricPairKernel	SymmetricPairKernel-class
computeROCandAUC	computeROCandAUC
ControlInformation	ControlInformation-class
ControlInformation-class	ControlInformation-class
cross.validation	performCrossValidation-methods
CrossValidation	performCrossValidation-methods
crossValidation	performCrossValidation-methods
CrossValidationResult	CrossValidationResult-class
CrossValidationResult-class	CrossValidationResult-class
CrossValidationResultAccessors	CrossValidationResultAccessors
cvResult	KBModelAccessors
cvResult,KBModel-method	KBModelAccessors
cvResult<-	KBModelAccessors
cvResult<-,KBModel-method	KBModelAccessors
DistanceWeightedKernel	positionDependentKernel
distanceWeightedKernel	positionDependentKernel
DNAVector	BioVector
DNAVector-class	BioVector-class
enhancerFB	kebabsData
evaluatePrediction	evaluatePrediction
ExplicitRepresentation	ExplicitRepresentation-class
ExplicitRepresentation-class	ExplicitRepresentation-class
ExplicitRepresentationAccessors	ExplicitRepresentationAccessors
ExplicitRepresentationDense	ExplicitRepresentation-class
ExplicitRepresentationDense-class	ExplicitRepresentation-class
ExplicitRepresentationSparse	ExplicitRepresentation-class
ExplicitRepresentationSparse-class	ExplicitRepresentation-class
expWeight	positionDependentKernel
featureWeights	KBModelAccessors
featureWeights,KBModel-method	KBModelAccessors
featureWeights<-	KBModelAccessors
featureWeights<-,KBModel-method	KBModelAccessors
folds	CrossValidationResultAccessors
folds,CrossValidationResult-method	CrossValidationResultAccessors
fpr	ROCDataAccessors
fpr,ROCData-method	ROCDataAccessors
fpr<-	ROCDataAccessors
fpr<-,ROCData-method	ROCDataAccessors
fullModel	ModelSelectionResultAccessors
fullModel,ModelSelectionResult-method	ModelSelectionResultAccessors
GappyPairKernel	GappyPairKernel-class
gappyPairKernel	gappyPairKernel
GappyPairKernel-class	GappyPairKernel-class
gaussWeight	positionDependentKernel
genRandBioSeqs	genRandBioSeqs
getExRep	explicitRepresentation
getExRepQuadratic	explicitRepresentation
getFeatureSpaceDimension	spectrumKernel
getFeatureSpaceDimension,ANY-method	spectrumKernel
getFeatureSpaceDimension,GappyPairKernel-method	gappyPairKernel
getFeatureSpaceDimension,MismatchKernel-method	mismatchKernel
getFeatureSpaceDimension,MotifKernel-method	motifKernel
getFeatureSpaceDimension,SpectrumKernel-method	spectrumKernel
getFeatureWeights	featureWeights
getKernelMatrix	sequenceKernel
getPredictionProfile	getPredictionProfile-methods
getPredictionProfile,BioVector-method	getPredictionProfile-methods
getPredictionProfile,XString-method	getPredictionProfile-methods
getPredictionProfile,XStringSet-method	getPredictionProfile-methods
getPredProfMixture	getPredProfMixture-methods
getPredProfMixture,BioVector-method	getPredProfMixture-methods
getPredProfMixture,XString-method	getPredProfMixture-methods
getPredProfMixture,XStringSet-method	getPredProfMixture-methods
getSVMSlotValue	KBModelAccessors
grid.search	performGridSearch
gridColumns	ModelSelectionResultAccessors
gridColumns,ModelSelectionResult-method	ModelSelectionResultAccessors
gridErrors	ModelSelectionResultAccessors
gridErrors,ModelSelectionResult-method	ModelSelectionResultAccessors
gridRows	ModelSelectionResultAccessors
gridRows,ModelSelectionResult-method	ModelSelectionResultAccessors
GridSearch	performGridSearch
gridSearch	performGridSearch
heatmap	heatmap-methods
heatmap,PredictionProfile,missing-method	heatmap-methods
heatmap,PredictionProfile-method	heatmap-methods
isUserDefined	sequenceKernel
isUserDefined,SequenceKernel-method	sequenceKernel
KBModel	KBModel-class
KBModel-class	KBModel-class
KBModelAccessors	KBModelAccessors
kbsvm	kbsvm-methods
kbsvm,BioVector-method	kbsvm-methods
kbsvm,ExplicitRepresentation-method	kbsvm-methods
kbsvm,KernelMatrix-method	kbsvm-methods
kbsvm,XStringSet-method	kbsvm-methods
KEBABS	kebabsOverview
KeBABS	kebabsOverview
kebabs	kebabsOverview
kebabsCollectInfo	kebabsCollectInfo
kebabsData	kebabsData
kebabsDemo	kebabsOverview
KernelMatrix	KernelMatrix-class
KernelMatrix-class	KernelMatrix-class
KernelMatrixAccessors	KernelMatrixAccessors
kernelParameters	sequenceKernel
kernelParameters,GappyPairKernel-method	sequenceKernel
kernelParameters,MismatchKernel-method	sequenceKernel
kernelParameters,MotifKernel-method	sequenceKernel
kernelParameters,SpectrumKernel-method	sequenceKernel
kernelParameters,SymmetricPair-method	sequenceKernel
kernelParameters,SymmetricPairKernel-method	sequenceKernel
kernelParameters-method	sequenceKernel
length	BioVector
length,BioVector-method	BioVector
linearKernel	LinearKernel
linWeight	positionDependentKernel
MismatchKernel	MismatchKernel-class
mismatchKernel	mismatchKernel
MismatchKernel-class	MismatchKernel-class
model.selection	performModelSelection
modelOffset	KBModelAccessors
modelOffset,KBModel-method	KBModelAccessors
modelOffset<-	KBModelAccessors
modelOffset<-,KBModel-method	KBModelAccessors
ModelSelection	performModelSelection
modelSelection	performModelSelection
ModelSelectionResult	ModelSelectionResult-class
ModelSelectionResult-class	ModelSelectionResult-class
ModelSelectionResultAccessors	ModelSelectionResultAccessors
modelSelResult	KBModelAccessors
modelSelResult,KBModel-method	KBModelAccessors
modelSelResult<-	KBModelAccessors
modelSelResult<-,KBModel-method	KBModelAccessors
MotifKernel	MotifKernel-class
motifKernel	motifKernel
MotifKernel-class	MotifKernel-class
names	BioVector
names,BioVector-method	BioVector
names<-	BioVector
names<-,BioVector-method	BioVector
performance	ModelSelectionResultAccessors
performance,CrossValidationResult-method	CrossValidationResultAccessors
performance,ModelSelectionResult-method	ModelSelectionResultAccessors
performCrossValidation	performCrossValidation-methods
performCrossValidation,ExplicitRepresentation-method	performCrossValidation-methods
performCrossValidation,KernelMatrix-method	performCrossValidation-methods
performGridSearch	performGridSearch
performModelSelection	performModelSelection
plot	plot-methods
plot,CrossValidationResult,missing-method	plot-methods
plot,CrossValidationResult-method	plot-methods
plot,ModelSelectionResult,missing-method	plot-methods
plot,ModelSelectionResult-method	plot-methods
plot,PredictionProfile,missing-method	plot-methods
plot,PredictionProfile-method	plot-methods
plot,ROCData,missing-method	plot-methods
plot,ROCData-method	plot-methods
PositionDependentKernel	positionDependentKernel
positionDependentKernel	positionDependentKernel
positionMetadata	positionDependentKernel
positionMetadata,BioVector-method	positionDependentKernel
positionMetadata,XStringSet-method	positionDependentKernel
positionMetadata<-	positionDependentKernel
positionMetadata<-,BioVector-method	positionDependentKernel
positionMetadata<-,XStringSet-method	positionDependentKernel
PositionSpecificKernel	positionDependentKernel
positionSpecificKernel	positionDependentKernel
predict	predict-methods
predict,KBModel-method	predict-methods
predict.KBModel	predict-methods
predict.kbsvm	predict-methods
PredictionProfile	PredictionProfile-class
PredictionProfile-class	PredictionProfile-class
PredictionProfileAccessors	PredictionProfileAccessors
predictSVM	SVMAccess
predictSVM,ExpicitRepresentation-method	SVMAccess
predictSVM,ExplicitRepresentation-method	SVMAccess
predictSVM,KernelMatrix-method	SVMAccess
predictSVM,missing-method	SVMAccess
predictSVM.KernelMatrix	SVMAccess
probabilityModel	KBModelAccessors
probabilityModel,KBModel-method	KBModelAccessors
probabilityModel<-	KBModelAccessors
probabilityModel<-,KBModel-method	KBModelAccessors
profiles	PredictionProfileAccessors
profiles,PredictionProfile-method	PredictionProfileAccessors
RNAVector	BioVector
RNAVector-class	BioVector-class
ROCData	ROCData-class
ROCData-class	ROCData-class
ROCDataAccessors	ROCDataAccessors
selGridCol	ModelSelectionResultAccessors
selGridCol,ModelSelectionResult-method	ModelSelectionResultAccessors
selGridRow	ModelSelectionResultAccessors
selGridRow,ModelSelectionResult-method	ModelSelectionResultAccessors
seqKernelAsChar	sequenceKernel
SequenceKernel	SequenceKernel-class
sequenceKernel	sequenceKernel
SequenceKernel-class	SequenceKernel-class
sequences	PredictionProfileAccessors
sequences,PredictionProfile-method	PredictionProfileAccessors
set	annotationSpecificKernel
show	show-methods
show,BioVector-method	show-methods
show,CrossValidationResult-method	show-methods
show,ExplicitRepresentationDense-method	show-methods
show,ExplicitRepresentationSparse-method	show-methods
show,GappyPairKernel-method	show-methods
show,KBModel-method	show-methods
show,MismatchKernel-method	show-methods
show,ModelSelectionResult-method	show-methods
show,MotifKernel-method	show-methods
show,PredictionProfile-method	show-methods
show,ROCData-method	show-methods
show,SpectrumKernel-method	show-methods
show,SVMInformation-method	show-methods
show,SymmetricPairKernel-method	show-methods
show.BioVector	show-methods
showAnnotatedSeq	annotationSpecificKernel
SpectrumKernel	SpectrumKernel-class
spectrumKernel	spectrumKernel
SpectrumKernel-class	SpectrumKernel-class
SVindex	KBModelAccessors
SVindex,KBModel-method	KBModelAccessors
SVindex<-	KBModelAccessors
SVindex<-,KBModel-method	KBModelAccessors
SVMInformation	SVMInformation-class
SVMInformation-class	SVMInformation-class
svmModel	KBModelAccessors
svmModel,KBModel-method	KBModelAccessors
svmModel<-	KBModelAccessors
svmModel<-,KBModel-method	KBModelAccessors
swdWeight	positionDependentKernel
SymmetricPairKernel	SymmetricPairKernel-class
symmetricPairKernel	symmetricPairKernel
SymmetricPairKernel-class	SymmetricPairKernel-class
TFBS	kebabsData
tpr	ROCDataAccessors
tpr,ROCData-method	ROCDataAccessors
tpr<-	ROCDataAccessors
tpr<-,ROCData-method	ROCDataAccessors
trainSVM	SVMAccess
trainSVM,ExplicitRepresentation-method	SVMAccess
trainSVM,KernelMatrix-method	SVMAccess
width	BioVector
width,BioVector-method	BioVector
yCC	kebabsData
yFB	kebabsData
[,BioVector,index,missing,ANY-method	BioVector
[,BioVector-method	BioVector
[,ExplicitRepresentation,index,index,ANY-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationDense,index,index,ANY-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationDense,index,missing,ANY-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationDense,missing,index,ANY-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationSparse,index,index,ANY-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationSparse,index,index,logical-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationSparse,index,index,missing-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationSparse,index,missing,ANY-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationSparse,index,missing,logical-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationSparse,index,missing,missing-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationSparse,missing,index,ANY-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationSparse,missing,index,logical-method	ExplicitRepresentationAccessors
[,ExplicitRepresentationSparse,missing,index,missing-method	ExplicitRepresentationAccessors
[,KernelMatrix,index,index,ANY-method	KernelMatrixAccessors
[,KernelMatrix,index,missing,ANY-method	KernelMatrixAccessors
[,KernelMatrix,missing,index,ANY-method	KernelMatrixAccessors
[,PredictionProfile,index,ANY,ANY-method	PredictionProfileAccessors
