SpectrumKernel-class {kebabs} | R Documentation |
Spectrum Kernel Class
Instances of this class represent a kernel object for the spectrum kernel. The class is derived from SequenceKernel.
k
length of the substrings considered by the kernel
r
exponent (for details see spectrumKernel)
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.