MismatchKernel-class: Mismatch Kernel Class

In kebabs: Kernel-Based Analysis Of Biological Sequences

Description

Mismatch Kernel Class

Details

Instances of this class represent a kernel object for the mismatch kernel. The class is derived from SequenceKernel.

Slots

k

length of the substrings considered by the kernel

m

maximum number of mismatches

r

exponent (for details see mismatchKernel)

annSpec

not used for mismatch kernel

distWeight

not used for mismatch kernel

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

not used for mismatch kernel

mixCoef

not used for mismatch kernel

Author(s)

Johannes Palme <[e-mail]>

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.

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