Gappy Pair Kernel Class

Description

Gappy Pair Kernel Class

Details

Instances of this class represent a kernel object for the gappy pair kernel. The kernel considers adjacent pairs of kmers with up to m irrelevant characters between the pair. The class is derived from SequenceKernel.

Slots

k

length of the substrings considered by the kernel

m

maximum number of irrelevant character between two kmers

r

exponent (for details see gappyPairKernel)

annSpec

when set the kernel evaluates annotation information

distWeight

distance weighting function or vector

normalized

data generated with this kernel object is normalized

exact

use exact character set for evaluation

ignoreLower

ignore lower case characters in the sequence

presence

consider only the presence of kmers not their counts

revComplement

consider a kmer and its reverse complement as the same feature

mixCoef

mixing coefficients for mixture kernel

Author(s)

Johannes Palme <kebabs@bioinf.jku.at>

References

http://www.bioinf.jku.at/software/kebabs

J. Palme, S. Hochreiter, and U. Bodenhofer (2015) KeBABS: an R package for kernel-based analysis of biological sequences. Bioinformatics, 31(15):2574-2576, 2015. DOI: 10.1093/bioinformatics/btv176.