A B C D E F G H I K L M N P R S T W Y misc
AAVector | DNAVector, RNAVector, AAVector Objects and BioVector Class |
AAVector-class | BioVector, DNAVector, RNAVector and AAVector Classes |
annotationCharset | Annotation Specific Kernel |
annotationCharset-method | Annotation Specific Kernel |
annotationMetadata | Annotation Specific Kernel |
annotationMetadata-method | Annotation Specific Kernel |
annotationMetadata<- | Annotation Specific Kernel |
annotationMetadata<--method | Annotation Specific Kernel |
AnnotationSpecificKernel | Annotation Specific Kernel |
annotationSpecificKernel | Annotation Specific Kernel |
as.character-method | DNAVector, RNAVector, AAVector Objects and BioVector Class |
as.KernelMatrix | KernelMatrix Accessors |
as.KernelMatrix-method | KernelMatrix Accessors |
auc | ROCData Accessors |
auc-method | ROCData Accessors |
auc<- | ROCData Accessors |
auc<--method | ROCData Accessors |
baselines | PredictionProfile Accessors |
baselines-method | PredictionProfile Accessors |
BioVector | DNAVector, RNAVector, AAVector Objects and BioVector Class |
BioVector-class | BioVector, DNAVector, RNAVector and AAVector Classes |
c-method | DNAVector, RNAVector, AAVector Objects and BioVector Class |
ccannot | KeBABS Sequence Data |
ccgroups | KeBABS Sequence Data |
ccseq | KeBABS Sequence Data |
character | Annotation Specific Kernel |
class:AAVector | BioVector, DNAVector, RNAVector and AAVector Classes |
class:BioVector | BioVector, DNAVector, RNAVector and AAVector Classes |
class:ControlInformation | KeBABS Control Information Class |
class:CrossValidationResult | Cross Validation Result Class |
class:DNAVector | BioVector, DNAVector, RNAVector and AAVector Classes |
class:ExplicitRepresentation | Explicit Representation Dense and Sparse Classes |
class:ExplicitRepresentationDense | Explicit Representation Dense and Sparse Classes |
class:ExplicitRepresentationSparse | Explicit Representation Dense and Sparse Classes |
class:GappyPairKernel | Gappy Pair Kernel Class |
class:KBModel | KeBABS Model Class |
class:KernelMatrix | Kernel Matrix Class |
class:MismatchKernel | Mismatch Kernel Class |
class:ModelSelectionResult | Model Selection Result Class |
class:MotifKernel | Motif Kernel Class |
class:PredictionProfile | Prediction Profile Class |
class:RNAVector | BioVector, DNAVector, RNAVector and AAVector Classes |
class:ROCData | ROC Data Class |
class:SequenceKernel | Sequence Kernel Class |
class:SpectrumKernel | Spectrum Kernel Class |
class:SVMInformation | SVM Information Class |
class:SymmetricPairKernel | Symmetric Pair Kernel Class |
computeROCandAUC | Compute Receiver Operating Characteristic And Area Under The Curve |
ControlInformation | KeBABS Control Information Class |
ControlInformation-class | KeBABS Control Information Class |
cross.validation | KeBABS Cross Validation |
CrossValidation | KeBABS Cross Validation |
crossValidation | KeBABS Cross Validation |
CrossValidationResult | Cross Validation Result Class |
CrossValidationResult-class | Cross Validation Result Class |
CrossValidationResultAccessors | CrossValidationResult Accessors |
cvResult | KBModel Accessors |
cvResult-method | KBModel Accessors |
cvResult<- | KBModel Accessors |
cvResult<--method | KBModel Accessors |
DistanceWeightedKernel | Position Dependent Kernel |
distanceWeightedKernel | Position Dependent Kernel |
DNAVector | DNAVector, RNAVector, AAVector Objects and BioVector Class |
DNAVector-class | BioVector, DNAVector, RNAVector and AAVector Classes |
enhancerFB | KeBABS Sequence Data |
evaluatePrediction | Evaluate Prediction |
ExplicitRepresentation | Explicit Representation Dense and Sparse Classes |
ExplicitRepresentation-class | Explicit Representation Dense and Sparse Classes |
ExplicitRepresentationAccessors | ExplicitRepresentation Accessors |
ExplicitRepresentationDense | Explicit Representation Dense and Sparse Classes |
ExplicitRepresentationDense-class | Explicit Representation Dense and Sparse Classes |
ExplicitRepresentationSparse | Explicit Representation Dense and Sparse Classes |
ExplicitRepresentationSparse-class | Explicit Representation Dense and Sparse Classes |
expWeight | Position Dependent Kernel |
featureWeights | KBModel Accessors |
featureWeights-method | KBModel Accessors |
featureWeights<- | KBModel Accessors |
featureWeights<--method | KBModel Accessors |
folds | CrossValidationResult Accessors |
folds-method | CrossValidationResult Accessors |
fpr | ROCData Accessors |
fpr-method | ROCData Accessors |
fpr<- | ROCData Accessors |
fpr<--method | ROCData Accessors |
fullModel | ModelSelectionResult Accessors |
fullModel-method | ModelSelectionResult Accessors |
GappyPairKernel | Gappy Pair Kernel Class |
gappyPairKernel | Gappy Pair Kernel |
GappyPairKernel-class | Gappy Pair Kernel Class |
gaussWeight | Position Dependent Kernel |
genRandBioSeqs | Generate Random Biological Sequences |
getExRep | Explict Representation |
getExRepQuadratic | Explict Representation |
getFeatureSpaceDimension | Spectrum Kernel |
getFeatureSpaceDimension-method | Gappy Pair Kernel |
getFeatureSpaceDimension-method | Mismatch Kernel |
getFeatureSpaceDimension-method | Motif Kernel |
getFeatureSpaceDimension-method | Spectrum Kernel |
getFeatureWeights | Feature Weights |
getKernelMatrix | Sequence Kernel |
getPredictionProfile | Calculation Of Predicition Profiles |
getPredictionProfile-method | Calculation Of Predicition Profiles |
getPredProfMixture | Calculation Of Predicition Profiles for Mixture Kernels |
getPredProfMixture-method | Calculation Of Predicition Profiles for Mixture Kernels |
getSVMSlotValue | KBModel Accessors |
grid.search | KeBABS Grid Search |
gridColumns | ModelSelectionResult Accessors |
gridColumns-method | ModelSelectionResult Accessors |
gridErrors | ModelSelectionResult Accessors |
gridErrors-method | ModelSelectionResult Accessors |
gridRows | ModelSelectionResult Accessors |
gridRows-method | ModelSelectionResult Accessors |
GridSearch | KeBABS Grid Search |
gridSearch | KeBABS Grid Search |
heatmap | Heatmap Methods |
heatmap-method | Heatmap Methods |
isUserDefined | Sequence Kernel |
isUserDefined-method | Sequence Kernel |
KBModel | KeBABS Model Class |
KBModel-class | KeBABS Model Class |
KBModelAccessors | KBModel Accessors |
kbsvm | KeBABS Training Methods |
kbsvm-method | KeBABS Training Methods |
KEBABS | kebabs |
KeBABS | kebabs |
kebabs | kebabs |
kebabsCollectInfo | Collect KeBABS Package Information |
kebabsData | KeBABS Sequence Data |
kebabsDemo | kebabs |
KernelMatrix | Kernel Matrix Class |
KernelMatrix-class | Kernel Matrix Class |
KernelMatrixAccessors | KernelMatrix Accessors |
kernelParameters | Sequence Kernel |
kernelParameters-method | Sequence Kernel |
length | DNAVector, RNAVector, AAVector Objects and BioVector Class |
length-method | DNAVector, RNAVector, AAVector Objects and BioVector Class |
linearKernel | Linear Kernel |
linWeight | Position Dependent Kernel |
MismatchKernel | Mismatch Kernel Class |
mismatchKernel | Mismatch Kernel |
MismatchKernel-class | Mismatch Kernel Class |
model.selection | KeBABS Model Selection |
modelOffset | KBModel Accessors |
modelOffset-method | KBModel Accessors |
modelOffset<- | KBModel Accessors |
modelOffset<--method | KBModel Accessors |
ModelSelection | KeBABS Model Selection |
modelSelection | KeBABS Model Selection |
ModelSelectionResult | Model Selection Result Class |
ModelSelectionResult-class | Model Selection Result Class |
ModelSelectionResultAccessors | ModelSelectionResult Accessors |
modelSelResult | KBModel Accessors |
modelSelResult-method | KBModel Accessors |
modelSelResult<- | KBModel Accessors |
modelSelResult<--method | KBModel Accessors |
MotifKernel | Motif Kernel Class |
motifKernel | Motif Kernel |
MotifKernel-class | Motif Kernel Class |
names | DNAVector, RNAVector, AAVector Objects and BioVector Class |
names-method | DNAVector, RNAVector, AAVector Objects and BioVector Class |
names<- | DNAVector, RNAVector, AAVector Objects and BioVector Class |
names<--method | DNAVector, RNAVector, AAVector Objects and BioVector Class |
performance | ModelSelectionResult Accessors |
performance-method | CrossValidationResult Accessors |
performance-method | ModelSelectionResult Accessors |
performCrossValidation | KeBABS Cross Validation |
performCrossValidation-method | KeBABS Cross Validation |
performGridSearch | KeBABS Grid Search |
performModelSelection | KeBABS Model Selection |
plot | Plot Prediction Profiles, Cross Validation Result, Grid Search Performance Parameters and Receiver Operating Characteristics |
plot-method | Plot Prediction Profiles, Cross Validation Result, Grid Search Performance Parameters and Receiver Operating Characteristics |
PositionDependentKernel | Position Dependent Kernel |
positionDependentKernel | Position Dependent Kernel |
positionMetadata | Position Dependent Kernel |
positionMetadata-method | Position Dependent Kernel |
positionMetadata<- | Position Dependent Kernel |
positionMetadata<--method | Position Dependent Kernel |
PositionSpecificKernel | Position Dependent Kernel |
positionSpecificKernel | Position Dependent Kernel |
predict | KeBABS Prediction Methods |
predict-method | KeBABS Prediction Methods |
predict.KBModel | KeBABS Prediction Methods |
predict.kbsvm | KeBABS Prediction Methods |
PredictionProfile | Prediction Profile Class |
PredictionProfile-class | Prediction Profile Class |
PredictionProfileAccessors | PredictionProfile Accessors |
predictSVM | SVM Access for Training and Prediction |
predictSVM-method | SVM Access for Training and Prediction |
predictSVM.KernelMatrix | SVM Access for Training and Prediction |
probabilityModel | KBModel Accessors |
probabilityModel-method | KBModel Accessors |
probabilityModel<- | KBModel Accessors |
probabilityModel<--method | KBModel Accessors |
profiles | PredictionProfile Accessors |
profiles-method | PredictionProfile Accessors |
RNAVector | DNAVector, RNAVector, AAVector Objects and BioVector Class |
RNAVector-class | BioVector, DNAVector, RNAVector and AAVector Classes |
ROCData | ROC Data Class |
ROCData-class | ROC Data Class |
ROCDataAccessors | ROCData Accessors |
selGridCol | ModelSelectionResult Accessors |
selGridCol-method | ModelSelectionResult Accessors |
selGridRow | ModelSelectionResult Accessors |
selGridRow-method | ModelSelectionResult Accessors |
seqKernelAsChar | Sequence Kernel |
SequenceKernel | Sequence Kernel Class |
sequenceKernel | Sequence Kernel |
SequenceKernel-class | Sequence Kernel Class |
sequences | PredictionProfile Accessors |
sequences-method | PredictionProfile Accessors |
set | Annotation Specific Kernel |
show | Display Various KeBABS Objects |
show-method | Display Various KeBABS Objects |
show.BioVector | Display Various KeBABS Objects |
showAnnotatedSeq | Annotation Specific Kernel |
SpectrumKernel | Spectrum Kernel Class |
spectrumKernel | Spectrum Kernel |
SpectrumKernel-class | Spectrum Kernel Class |
SVindex | KBModel Accessors |
SVindex-method | KBModel Accessors |
SVindex<- | KBModel Accessors |
SVindex<--method | KBModel Accessors |
SVMInformation | SVM Information Class |
SVMInformation-class | SVM Information Class |
svmModel | KBModel Accessors |
svmModel-method | KBModel Accessors |
svmModel<- | KBModel Accessors |
svmModel<--method | KBModel Accessors |
swdWeight | Position Dependent Kernel |
SymmetricPairKernel | Symmetric Pair Kernel Class |
symmetricPairKernel | Symmetric Pair Kernel |
SymmetricPairKernel-class | Symmetric Pair Kernel Class |
TFBS | KeBABS Sequence Data |
tpr | ROCData Accessors |
tpr-method | ROCData Accessors |
tpr<- | ROCData Accessors |
tpr<--method | ROCData Accessors |
trainSVM | SVM Access for Training and Prediction |
trainSVM-method | SVM Access for Training and Prediction |
width | DNAVector, RNAVector, AAVector Objects and BioVector Class |
width-method | DNAVector, RNAVector, AAVector Objects and BioVector Class |
yCC | KeBABS Sequence Data |
yFB | KeBABS Sequence Data |
%*%-method | ExplicitRepresentation Accessors |
[-method | DNAVector, RNAVector, AAVector Objects and BioVector Class |
[-method | ExplicitRepresentation Accessors |
[-method | KernelMatrix Accessors |
[-method | PredictionProfile Accessors |