kebabs: Kernel-Based Analysis Of Biological Sequences

Share:

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.

Author
Johannes Palme
Date of publication
None
Maintainer
Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
License
GPL (>= 2.1)
Version
1.8.0
URLs

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