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.

AuthorJohannes Palme
Date of publicationNone
MaintainerUlrich Bodenhofer <bodenhofer@bioinf.jku.at>
LicenseGPL (>= 2.1)
Version1.8.0
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

Files in this package

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

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