API for kebabs
Kernel-Based Analysis Of Biological Sequences

Global functions
%*%,dgRMatrix,numeric-method	Man page
%*%,matrix,dgRMatrix-method	Man page
.onLoad	Source code
.onUnload	Source code
AAVector	Man page Source code
AAVector-class	Man page
AnnotationSpecificKernel	Man page
BioVector	Man page
BioVector-class	Man page
ControlInformation	Man page
ControlInformation-class	Man page
CrossValidation	Man page
CrossValidationResult	Man page
CrossValidationResult-class	Man page
CrossValidationResultAccessors	Man page
DNAVector	Man page Source code
DNAVector-class	Man page
DistanceWeightedKernel	Man page
ExplicitRepresentation	Man page
ExplicitRepresentation-class	Man page
ExplicitRepresentationAccessors	Man page
ExplicitRepresentationDense	Man page
ExplicitRepresentationDense-class	Man page
ExplicitRepresentationSparse	Man page
ExplicitRepresentationSparse-class	Man page
GappyPairKernel	Man page
GappyPairKernel-class	Man page
GridSearch	Man page
KBModel	Man page
KBModel-class	Man page
KBModelAccessors	Man page
KEBABS	Man page
KeBABS	Man page
KernelMatrix	Man page
KernelMatrix-class	Man page
KernelMatrixAccessors	Man page
MismatchKernel	Man page
MismatchKernel-class	Man page
ModelSelection	Man page
ModelSelectionResult	Man page
ModelSelectionResult-class	Man page
ModelSelectionResultAccessors	Man page
MotifKernel	Man page
MotifKernel-class	Man page
PositionDependentKernel	Man page
PositionSpecificKernel	Man page
PredictionProfile	Man page
PredictionProfile-class	Man page
PredictionProfileAccessors	Man page
RNAVector	Man page Source code
RNAVector-class	Man page
ROCData	Man page
ROCData-class	Man page
ROCDataAccessors	Man page
SVMInformation	Man page
SVMInformation-class	Man page
SVindex	Man page
SVindex,KBModel-method	Man page
SVindex<-	Man page
SVindex<-,KBModel-method	Man page
SequenceKernel	Man page
SequenceKernel-class	Man page
SpectrumKernel	Man page
SpectrumKernel-class	Man page
SymmetricPairKernel	Man page
SymmetricPairKernel-class	Man page
TFBS	Man page
[,BioVector,index,missing,ANY-method	Man page
[,BioVector-method	Man page
[,ExplicitRepresentation,index,index,ANY-method	Man page
[,ExplicitRepresentationDense,index,index,ANY-method	Man page
[,ExplicitRepresentationDense,index,missing,ANY-method	Man page
[,ExplicitRepresentationDense,missing,index,ANY-method	Man page
[,ExplicitRepresentationSparse,index,index,ANY-method	Man page
[,ExplicitRepresentationSparse,index,index,logical-method	Man page
[,ExplicitRepresentationSparse,index,index,missing-method	Man page
[,ExplicitRepresentationSparse,index,missing,ANY-method	Man page
[,ExplicitRepresentationSparse,index,missing,logical-method	Man page
[,ExplicitRepresentationSparse,index,missing,missing-method	Man page
[,ExplicitRepresentationSparse,missing,index,ANY-method	Man page
[,ExplicitRepresentationSparse,missing,index,logical-method	Man page
[,ExplicitRepresentationSparse,missing,index,missing-method	Man page
[,KernelMatrix,index,index,ANY-method	Man page
[,KernelMatrix,index,missing,ANY-method	Man page
[,KernelMatrix,missing,index,ANY-method	Man page
[,PredictionProfile,index,ANY,ANY-method	Man page
addOrReplaceSVMParameters	Source code
annotationCharset	Man page
annotationCharset,BioVector-method	Man page
annotationCharset,XStringSet-method	Man page
annotationMetadata	Man page
annotationMetadata,BioVector-method	Man page
annotationMetadata,XStringSet-method	Man page
annotationMetadata<-	Man page
annotationMetadata<-,BioVector-method	Man page
annotationMetadata<-,XStringSet-method	Man page
annotationSpecificKernel	Man page
anyUserDefinedKernel	Source code
as.KernelMatrix	Man page
as.KernelMatrix,matrix-method	Man page
as.character,BioVector-method	Man page
asERD.ExplicitRepresentationSparse	Source code
asERS.ExplicitRepresentationDense	Source code
asKernelMatrix	Source code
asmatrix.ExplicitRepresentationSparse	Source code
auc	Man page
auc,ROCData-method	Man page
auc<-	Man page
auc<-,ROCData-method	Man page
baselines	Man page
baselines,PredictionProfile-method	Man page
c,BioVector-method	Man page
ccannot	Man page
ccgroups	Man page
ccseq	Man page
character	Man page
checkKBSVMParams	Source code
checkModelSelParams	Source code
checkSVMPackagePresence	Source code
class:AAVector	Man page
class:BioVector	Man page
class:ControlInformation	Man page
class:CrossValidationResult	Man page
class:DNAVector	Man page
class:ExplicitRepresentation	Man page
class:ExplicitRepresentationDense	Man page
class:ExplicitRepresentationSparse	Man page
class:GappyPairKernel	Man page
class:KBModel	Man page
class:KernelMatrix	Man page
class:MismatchKernel	Man page
class:ModelSelectionResult	Man page
class:MotifKernel	Man page
class:PredictionProfile	Man page
class:RNAVector	Man page
class:ROCData	Man page
class:SVMInformation	Man page
class:SequenceKernel	Man page
class:SpectrumKernel	Man page
class:SymmetricPairKernel	Man page
cleanupKebabs	Source code
computeROCandAUC	Man page Source code
convertSVMParameters	Source code
convertSymmetricMatrixToVector	Source code
cross.validation	Man page
crossValidation	Man page
cvResult	Man page
cvResult,KBModel-method	Man page
cvResult<-	Man page
cvResult<-,KBModel-method	Man page
detectInstalledPackages	Source code
distWeightKernelToString	Source code
distanceWeightedKernel	Man page
enhancerFB	Man page
ersTransposedAsdgCMatrix	Source code
evaluatePrediction	Man page Source code
expWeight	Man page Source code
featureWeights	Man page
featureWeights,KBModel-method	Man page
featureWeights<-	Man page
featureWeights<-,KBModel-method	Man page
folds	Man page
folds,CrossValidationResult-method	Man page
formatSVMSlotValue	Source code
fpr	Man page
fpr,ROCData-method	Man page
fpr<-	Man page
fpr<-,ROCData-method	Man page
fullModel	Man page
fullModel,ModelSelectionResult-method	Man page
gappyPairKernel	Man page Source code
gappyPairProcessing	Source code
gaussWeight	Man page Source code
genRandBioSeqs	Man page Source code
generateRuntimeMessage	Source code
getAnnotationCharset.seq	Source code
getAnnotationMetadata.seq	Source code
getBioCharset	Source code
getExRep	Man page Source code
getExRepQuadratic	Man page Source code
getExRepQuadraticSparse	Source code
getFeatureSpaceDimension	Man page
getFeatureSpaceDimension,ANY-method	Man page
getFeatureSpaceDimension,GappyPairKernel-method	Man page
getFeatureSpaceDimension,MismatchKernel-method	Man page
getFeatureSpaceDimension,MotifKernel-method	Man page
getFeatureSpaceDimension,SpectrumKernel-method	Man page
getFeatureSpaceDimension.ANY	Source code
getFeatureSpaceDimension.gappy	Source code
getFeatureSpaceDimension.motif	Source code
getFeatureSpaceDimension.spectrum	Source code
getFeatureSpaceDimension.stringkernel	Source code
getFeatureWeights	Man page Source code
getFeatureWeightsPosDep	Source code
getFeatureWeightsPosIndep	Source code
getKernelMatrix	Man page Source code
getMulticlassType	Source code
getNoOfElementsOfSeqRep	Source code
getPositionMetadata.seq	Source code
getPredProfMixture	Man page
getPredProfMixture,BioVector-method	Man page
getPredProfMixture,XString-method	Man page
getPredProfMixture,XStringSet-method	Man page
getPredProfMixture.BioVectorOrXSS	Source code
getPredProfMixture.XString	Source code
getPredictionProfile	Man page
getPredictionProfile,BioVector-method	Man page
getPredictionProfile,XString-method	Man page
getPredictionProfile,XStringSet-method	Man page
getPredictionProfile.BioVectorOrXSS	Source code
getPredictionProfile.XString	Source code
getProbability	Source code
getSVMSlotValue	Man page Source code
getSingleFeaturesFromQuadratic	Source code
getSlidingWindowAverage	Source code
getSlotValue	Source code
getSupportedPackages	Source code
grid.search	Man page
gridColumns	Man page
gridColumns,ModelSelectionResult-method	Man page
gridErrors	Man page
gridErrors,ModelSelectionResult-method	Man page
gridRows	Man page
gridRows,ModelSelectionResult-method	Man page
gridSearch	Man page
heatmap	Man page
heatmap,PredictionProfile,missing-method	Man page
heatmap,PredictionProfile-method	Man page
heatmap.predprof	Source code
initKebabs	Source code
isClassification	Source code
isPkgInstalled	Source code
isSingleInteger	Source code
isSingleNumber	Source code
isSingleString	Source code
isTRUEorFALSE	Source code
isUserDefined	Man page
isUserDefined,SequenceKernel-method	Man page
kbsvm	Man page
kbsvm,BioVector-method	Man page
kbsvm,ExplicitRepresentation-method	Man page
kbsvm,KernelMatrix-method	Man page
kbsvm,XStringSet-method	Man page
kbsvm.ExplicitRep	Source code
kbsvm.KernelMatrix	Source code
kbsvm.kernelMatrix	Source code
kbsvm.seqs	Source code
kebabs	Man page
kebabsCollectInfo	Man page Source code
kebabsData	Man page
kebabsDemo	Man page Source code
kernelParameters	Man page
kernelParameters,GappyPairKernel-method	Man page
kernelParameters,MismatchKernel-method	Man page
kernelParameters,MotifKernel-method	Man page
kernelParameters,SpectrumKernel-method	Man page
kernelParameters,SymmetricPair-method	Man page
kernelParameters,SymmetricPairKernel-method	Man page
kernelParameters-method	Man page
length	Man page
length,BioVector-method	Man page
linWeight	Man page Source code
linearKernel	Man page Source code
listToString	Source code
loadSVMPackages	Source code
mapFeatureVector	Source code
mapModelParamName	Source code
mapSVMParamName	Source code
mismatchKernel	Man page Source code
mismatchProcessing	Source code
model.selection	Man page
modelOffset	Man page
modelOffset,KBModel-method	Man page
modelOffset<-	Man page
modelOffset<-,KBModel-method	Man page
modelSelResult	Man page
modelSelResult,KBModel-method	Man page
modelSelResult<-	Man page
modelSelResult<-,KBModel-method	Man page
modelSelection	Man page
motifKernel	Man page Source code
motifProcessing	Source code
names	Man page
names,BioVector-method	Man page
names<-	Man page
names<-,BioVector-method	Man page
performCrossValidation	Man page
performCrossValidation,ExplicitRepresentation-method	Man page
performCrossValidation,KernelMatrix-method	Man page
performCrossValidation.ExplicitRep	Source code
performCrossValidation.KernelMatrix	Source code
performCrossValidation.kernelMatrix	Source code
performGridSearch	Man page Source code
performModelSelection	Man page Source code
performance	Man page
performance,CrossValidationResult-method	Man page
performance,ModelSelectionResult-method	Man page
performance.CrossValidationResult	Source code
performance.ModelSelectionResult	Source code
plot	Man page
plot,CrossValidationResult,missing-method	Man page
plot,CrossValidationResult-method	Man page
plot,ModelSelectionResult,missing-method	Man page
plot,ModelSelectionResult-method	Man page
plot,PredictionProfile,missing-method	Man page
plot,PredictionProfile-method	Man page
plot,ROCData,missing-method	Man page
plot,ROCData-method	Man page
plot.cvResult	Source code
plot.performance	Source code
plot.roc	Source code
plotPredictionProfile.Missing	Source code
positionDependentKernel	Man page
positionMetadata	Man page
positionMetadata,BioVector-method	Man page
positionMetadata,XStringSet-method	Man page
positionMetadata<-	Man page
positionMetadata<-,BioVector-method	Man page
positionMetadata<-,XStringSet-method	Man page
positionSpecificKernel	Man page
predict	Man page
predict,KBModel-method	Man page
predict.FeatureWeights	Source code
predict.KBModel	Man page Source code
predict.NonFeatureWeights	Source code
predict.PositionDependent	Source code
predict.kbsvm	Man page
predictSVM	Man page
predictSVM,ExpicitRepresentation-method	Man page
predictSVM,ExplicitRepresentation-method	Man page
predictSVM,KernelMatrix-method	Man page
predictSVM,missing-method	Man page
predictSVM.ExRep	Source code
predictSVM.KernelMatrix	Man page Source code
predictSVM.missing	Source code
probabilityModel	Man page
probabilityModel,KBModel-method	Man page
probabilityModel<-	Man page
probabilityModel<-,KBModel-method	Man page
profiles	Man page
profiles,PredictionProfile-method	Man page
selGridCol	Man page
selGridCol,ModelSelectionResult-method	Man page
selGridRow	Man page
selGridRow,ModelSelectionResult-method	Man page
selectSVMMethod	Source code
seqKernelAsChar	Man page Source code
sequenceKernel	Man page
sequences	Man page
sequences,PredictionProfile-method	Man page
set	Man page
setAnnotationMetadata.seq	Source code
setPositionMetadata.seq	Source code
show	Man page
show,BioVector-method	Man page
show,CrossValidationResult-method	Man page
show,ExplicitRepresentationDense-method	Man page
show,ExplicitRepresentationSparse-method	Man page
show,GappyPairKernel-method	Man page
show,KBModel-method	Man page
show,MismatchKernel-method	Man page
show,ModelSelectionResult-method	Man page
show,MotifKernel-method	Man page
show,PredictionProfile-method	Man page
show,ROCData-method	Man page
show,SVMInformation-method	Man page
show,SpectrumKernel-method	Man page
show,SymmetricPairKernel-method	Man page
show.BioVector	Man page Source code
show.BioVectorSeq	Source code
show.PredictionProfile	Source code
showAnnotatedSeq	Man page Source code
sortWith_LC_Collate_C	Source code
spectrumKernel	Man page Source code
spectrumProcessing	Source code
subsetERSFeature	Source code
subsetERSSample	Source code
subsetERSSampleFeature	Source code
subsetSeqRep	Source code
supportsExplicitRep	Source code
svmModel	Man page
svmModel,KBModel-method	Man page
svmModel<-	Man page
svmModel<-,KBModel-method	Man page
svmSupportsOnlyExplicitRep	Source code
swdWeight	Man page Source code
symmPairProcessing	Source code
symmetricPairKernel	Man page Source code
toSeqSnippet	Source code
tpr	Man page
tpr,ROCData-method	Man page
tpr<-	Man page
tpr<-,ROCData-method	Man page
trainSVM	Man page
trainSVM,ExplicitRepresentation-method	Man page
trainSVM,KernelMatrix-method	Man page
trainSVM.KernelMatrix	Source code
trainSVM.explicitRep	Source code
unifyPredictionOutput	Source code
verbM	Source code
width	Man page
width,BioVector-method	Man page
yCC	Man page
yFB	Man page