kebabs: Kernel-Based Analysis Of Biological Sequences

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("kebabs")
AuthorJohannes Palme
Bioconductor views Classification Clustering Regression SupportVectorMachine
Date of publicationNone
MaintainerUlrich Bodenhofer <bodenhofer@bioinf.jku.at>
LicenseGPL (>= 2.1)
Version1.8.1
http://www.bioinf.jku.at/software/kebabs/

View on Bioconductor

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

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Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.