kebabs: Kernel-Based Analysis Of Biological Sequences
Version 1.10.0

The package provides functionality for kernel-based analysis of DNA, RNA, and amino acid sequences via SVM-based methods. As core functionality, kebabs implements following sequence kernels: spectrum kernel, mismatch kernel, gappy pair kernel, and motif kernel. Apart from an efficient implementation of standard position-independent functionality, the kernels are extended in a novel way to take the position of patterns into account for the similarity measure. Because of the flexibility of the kernel formulation, other kernels like the weighted degree kernel or the shifted weighted degree kernel with constant weighting of positions are included as special cases. An annotation-specific variant of the kernels uses annotation information placed along the sequence together with the patterns in the sequence. The package allows for the generation of a kernel matrix or an explicit feature representation in dense or sparse format for all available kernels which can be used with methods implemented in other R packages. With focus on SVM-based methods, kebabs provides a framework which simplifies the usage of existing SVM implementations in kernlab, e1071, and LiblineaR. Binary and multi-class classification as well as regression tasks can be used in a unified way without having to deal with the different functions, parameters, and formats of the selected SVM. As support for choosing hyperparameters, the package provides cross validation - including grouped cross validation, grid search and model selection functions. For easier biological interpretation of the results, the package computes feature weights for all SVMs and prediction profiles which show the contribution of individual sequence positions to the prediction result and indicate the relevance of sequence sections for the learning result and the underlying biological functions.

AuthorJohannes Palme
Bioconductor views Classification Clustering Regression SupportVectorMachine
Date of publicationNone
MaintainerUlrich Bodenhofer <bodenhofer@bioinf.jku.at>
LicenseGPL (>= 2.1)
Version1.10.0
URL http://www.bioinf.jku.at/software/kebabs/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("kebabs")

Popular man pages

explicitRepresentation: Explict Representation
GappyPairKernel-class: Gappy Pair Kernel Class
getPredictionProfile-methods: Calculation Of Predicition Profiles
kebabsData: KeBABS Sequence Data
LinearKernel: Linear Kernel
positionDependentKernel: Position Dependent Kernel
sequenceKernel: Sequence Kernel
See all...

All man pages Function index File listing

Man pages

annotationSpecificKernel: Annotation Specific Kernel
BioVector: DNAVector, RNAVector, AAVector Objects and BioVector Class
BioVector-class: BioVector, DNAVector, RNAVector and AAVector Classes
computeROCandAUC: Compute Receiver Operating Characteristic And Area Under The...
ControlInformation-class: KeBABS Control Information Class
CrossValidationResultAccessors: CrossValidationResult Accessors
CrossValidationResult-class: Cross Validation Result Class
evaluatePrediction: Evaluate Prediction
explicitRepresentation: Explict Representation
ExplicitRepresentationAccessors: ExplicitRepresentation Accessors
ExplicitRepresentation-class: Explicit Representation Dense and Sparse Classes
featureWeights: Feature Weights
gappyPairKernel: Gappy Pair Kernel
GappyPairKernel-class: Gappy Pair Kernel Class
genRandBioSeqs: Generate Random Biological Sequences
getPredictionProfile-methods: Calculation Of Predicition Profiles
getPredProfMixture-methods: Calculation Of Predicition Profiles for Mixture Kernels
heatmap-methods: Heatmap Methods
KBModelAccessors: KBModel Accessors
KBModel-class: KeBABS Model Class
kbsvm-methods: KeBABS Training Methods
kebabsCollectInfo: Collect KeBABS Package Information
kebabsData: KeBABS Sequence Data
kebabsOverview: kebabs
KernelMatrixAccessors: KernelMatrix Accessors
KernelMatrix-class: Kernel Matrix Class
LinearKernel: Linear Kernel
mismatchKernel: Mismatch Kernel
MismatchKernel-class: Mismatch Kernel Class
ModelSelectionResultAccessors: ModelSelectionResult Accessors
ModelSelectionResult-class: Model Selection Result Class
motifKernel: Motif Kernel
MotifKernel-class: Motif Kernel Class
performCrossValidation-methods: KeBABS Cross Validation
performGridSearch: KeBABS Grid Search
performModelSelection: KeBABS Model Selection
plot-methods: Plot Prediction Profiles, Cross Validation Result, Grid...
positionDependentKernel: Position Dependent Kernel
PredictionProfileAccessors: PredictionProfile Accessors
PredictionProfile-class: Prediction Profile Class
predict-methods: KeBABS Prediction Methods
ROCDataAccessors: ROCData Accessors
ROCData-class: ROC Data Class
sequenceKernel: Sequence Kernel
SequenceKernel-class: Sequence Kernel Class
show-methods: Display Various KeBABS Objects
spectrumKernel: Spectrum Kernel
SpectrumKernel-class: Spectrum Kernel Class
SVMAccess: SVM Access for Training and Prediction
SVMInformation-class: SVM Information Class
symmetricPairKernel: Symmetric Pair Kernel
SymmetricPairKernel-class: Symmetric Pair Kernel Class

Functions

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
\%*\%,dgRMatrix,numeric-method Man page
\%*\%,matrix,dgRMatrix-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
isLeaf.local 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
memberDend.local Source code
midCacheDend.local Source code
midDend.local 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
onLoad Source code
onUnload Source code
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
predict.svmd Source code
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
revDend.local Source code
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
svmd Source code
svmd.default Source code
svmd.formula 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

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/access-methods.R
R/annotationSpecificKernel.R
R/coerce-methods.R
R/explicitRepresentation.R
R/featureWeights.R
R/gappyPair.R
R/gridSearch.R
R/heatmap-methods.R
R/kbsvm-methods.R
R/kebabs.R
R/kebabsData.R
R/kebabsDemo.R
R/mismatch.R
R/modelSelection.R
R/motif.R
R/parameters.R
R/performCrossValidation-methods.R
R/plot-methods.R
R/positionDependentKernel.R
R/predict-methods.R
R/predictionProfile.R
R/predictsvm-methods.R
R/runtimeMessage.R
R/sequenceKernel.R
R/show-methods.R
R/spectrum.R
R/svm.R
R/svmModel.R
R/symmetricPair.R
R/trainsvm-methods.R
R/utils.R
R/zzz.R
build
build/vignette.rds
data
data/CCoil.RData
data/TFBS.RData
data/datalist
inst
inst/CITATION
inst/COPYRIGHT
inst/NEWS
inst/doc
inst/doc/kebabs.R
inst/doc/kebabs.Rnw
inst/doc/kebabs.pdf
inst/examples
inst/examples/UserDefinedSequenceKernel
inst/examples/UserDefinedSequenceKernel/SpectrumKernlabKernel
inst/examples/UserDefinedSequenceKernel/SpectrumKernlabKernel/RunKernel.R
inst/examples/UserDefinedSequenceKernel/SpectrumKernlabKernel/SpectrumKernlabKernel.R
man
man/BioVector-class.Rd
man/BioVector.Rd
man/ControlInformation-class.Rd
man/CrossValidationResult-class.Rd
man/CrossValidationResultAccessors.Rd
man/ExplicitRepresentation-class.Rd
man/ExplicitRepresentationAccessors.Rd
man/GappyPairKernel-class.Rd
man/KBModel-class.Rd
man/KBModelAccessors.Rd
man/KernelMatrix-class.Rd
man/KernelMatrixAccessors.Rd
man/LinearKernel.Rd
man/MismatchKernel-class.Rd
man/ModelSelectionResult-class.Rd
man/ModelSelectionResultAccessors.Rd
man/MotifKernel-class.Rd
man/PredictionProfile-class.Rd
man/PredictionProfileAccessors.Rd
man/ROCData-class.Rd
man/ROCDataAccessors.Rd
man/SVMAccess.Rd
man/SVMInformation-class.Rd
man/SequenceKernel-class.Rd
man/SpectrumKernel-class.Rd
man/SymmetricPairKernel-class.Rd
man/annotationSpecificKernel.Rd
man/computeROCandAUC.Rd
man/evaluatePrediction.Rd
man/explicitRepresentation.Rd
man/featureWeights.Rd
man/gappyPairKernel.Rd
man/genRandBioSeqs.Rd
man/getPredProfMixture-methods.Rd
man/getPredictionProfile-methods.Rd
man/heatmap-methods.Rd
man/kbsvm-methods.Rd
man/kebabsCollectInfo.Rd
man/kebabsData.Rd
man/kebabsOverview.Rd
man/mismatchKernel.Rd
man/motifKernel.Rd
man/performCrossValidation-methods.Rd
man/performGridSearch.Rd
man/performModelSelection.Rd
man/plot-methods.Rd
man/positionDependentKernel.Rd
man/predict-methods.Rd
man/sequenceKernel.Rd
man/show-methods.Rd
man/spectrumKernel.Rd
man/symmetricPairKernel.Rd
src
src/Biostrings_stubs.c
src/BitArray.h
src/ByteStringVector.c
src/ByteStringVector.h
src/ExplicitRepC.cpp
src/ExplicitRepC.h
src/FeatureVectorC.h
src/FeatureWeightsPosDepC.cpp
src/FeatureWeightsPosDepC.h
src/GappyPairC.cpp
src/GappyPairC.h
src/IRanges_stubs.c
src/IntegerPowers64.h
src/Kebabs.h
src/KernelUtils.cpp
src/KernelUtils.h
src/MismatchC.cpp
src/MismatchC.h
src/MotifC.cpp
src/MotifC.h
src/PredictionC.cpp
src/PredictionC.h
src/PredictionProfileC.cpp
src/PredictionProfileC.h
src/R_init_kebabs.cpp
src/Rsvm.c
src/SparseMatrixHash.cpp
src/SparseMatrixHash.h
src/SpectrumC.cpp
src/SpectrumC.h
src/SymmetricPairC.cpp
src/SymmetricPairC.h
src/Utils.cpp
src/Utils.h
src/XVector_stubs.c
src/khash.h
src/ksort.h
src/svm.cpp
src/svm.h
vignettes
vignettes/Heatmap.png
vignettes/JKU_EN_noName.pdf
vignettes/bioinf-article.txi
vignettes/bioinf-bar.png
vignettes/bioinf.cls
vignettes/kebabs.Rnw
vignettes/literature.bib
vignettes/natbib.sty
vignettes/plainnat.bst
kebabs documentation built on May 20, 2017, 9:23 p.m.

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