GappyPairKernel-class {kebabs} | R Documentation

## 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.

[Package kebabs version 1.20.0 Index]