Description:

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.

Changes to previous version:

• importing apcluster package for avoiding method clashes
• improved and completed change history in inst/NEWS and package vignette

BibTeX Entry: Download

Corresponding Paper BibTeX Entry: Download

Supported Operating Systems: Platform Independent

Data Formats: Any Format Supported By R

Tags: Bioinformatics, Support Vector Machine, Sequence Analysis, Classification, Kernels, Kernel Methods, Supervised Learning

Archive: download here

Other available revisons

Version	Changelog	Date
1.5.4	importing apcluster package for avoiding method clashes improved and completed change history in inst/NEWS and package vignette	July 28, 2017, 09:55:04
1.5.3	correction in prediction via feature weights for very large sparse explicit representation adaption of vignette template vignette engine changed from Sweave to knitr	July 28, 2017, 09:53:34
1.5.2	correction in distance weights for mixed distance weighted spectrum and gappy pair kernel allow featureWeights as numeric vector for method getPredictionProfile correction for plot of single prediction profile without legend change of copyright note namespace fixes	July 28, 2017, 09:52:15
1.5.1	new method to compute prediction profiles from models trained with mixture kernels correction for position specific kernel with offsets corrections for prediction profile of motif kernel additional hint on help page of kbsvm	July 28, 2017, 09:50:11
1.4.1	new method to compute prediction profiles from models trained with mixture kernels correction for position specific kernel with offsets corrections for prediction profile of motif kernel additional hint on help page of kbsvm	November 3, 2015, 11:33:46
1.4.0	correction of Ubuntu problem with realloc for 0 elements in linearKernel generating a sparse empty kernel matrix correction of problem with feature weights and prediction profiles for position specific gappy pair kernel correction of problem with feature weights and prediction profiles for position specific motif kernel corrections for feature weights, prediction via feature weights and prediction profile for distance weighted kernels update of KeBABS citation	October 16, 2015, 13:07:14
1.2.3	new export kebabsCollectInfo for collection of package info update of version dependency to Biostrings, XVector, S4Vector correction for leading + or - in factor label change of bibtex style sheet in vignette to plainnat.bst	May 26, 2015, 10:55:44
1.2.2	correction of error in kernel lists user defined sequence kernel example SpectrumKernlabKernel moved to separate directory	May 26, 2015, 10:55:06
1.2.1	correction of error in model selection for processing via dense LIBSVM remove problem in check for loading of SparseM	April 23, 2015, 13:55:32
1.2.0	inclusion of dense LIBSVM 3.20 for dense kernel matrix support to provide a reliable way for training with kernel matrices new accessors folds and performance for CrossValidationResult removed fold performance from show of CV result adaptions for user defined sequence kernel with new export isUserDefined, example in inst/examples/UserDefinedKernel correction of errors with position offset for position specific kernels computation of AUC via trapezoidal rule changes for auto mode in CV, grid search, model selection check for non-negative mixing coefficients in spectrum and gappy pair kernel build warnings on Windows removed added definition of performance parameters for binary and multiclass classification to vignette update of citation file and reference section in help pages	April 17, 2015, 21:15:37
1.0.5	new accessors selGridRow, selGridCol and fullModel for class ModelSelectionResult change of naming of feature weights because of change in LiblineaR 1.94-2 GCC warnings in Linux removed	March 4, 2015, 22:34:11
1.0.4	change in LiblineaR - upgrade to LIBLINEAR 1.94 in function LiblineaR the parameter labels was renamed to target correction in model selection for performance parameters minor changes in help pages minor changes in vignette	February 10, 2015, 13:26:20
1.0.3	extension of function linearKernel to optionally return a sparse kernel matrix new accessor SVindex for class KBModel error correction in subsetting of sparse explicit representation for head / tail error correction of vector length overflow in sparse explicit representation for very large number of sequences in spectrum, gappy pair and motif kernel error correction for training with position specific kernel and computation of feature weights error correction in coercion of kernel to character for distance weighting error correction in subsetting of prediction profile error correction in spectrum, gappy pair and motif kernel for kernel matrix - last feature was missing in kernel value in rare situations error correction and minor C code changes for mismatch kernel check uniqueness of motifs in motif kernel build warnings on Windows removed minor changes in help pages change name of vignette Rnw to lowercase minor changes in vignette	January 28, 2015, 10:19:33
1.0.2	a few C code changes for mismatch kernel correction of MCC correction of computation of feature weights for LiblineaR with more than 3 classes	December 4, 2014, 09:15:24
1.0.1	correction for cross validation with factor label correction for storing prob model in kebabs model for kernlab removal of clang warnings for unused functions	December 1, 2014, 12:08:31
1.0.0	Initial Announcement on mloss.org.	November 7, 2014, 14:17:57

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