GappyPairKernel-class: Gappy Pair Kernel Class
In kebabs: Kernel-Based Analysis Of Biological Sequences

Description Details Slots Author(s) References

Gappy Pair Kernel Class

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.

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

Johannes Palme <kebabs@bioinf.jku.at>

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.

kebabs documentation built on Nov. 8, 2020, 7:38 p.m.