kebabs (version 1.2.3)

show.BioVector: Display Various KeBABS Objects

Description

Display methods for BioVector, SpectrumKernel, MismatchKernel, GappyPairKernel, MotifKernel, SymmetricPairKernel, ExplicitRepresentationDense, ExplicitRepresentationSparse, PredictionProfile, CrossValidationResult, ModelSelectionResult, SVMInformation and KBModel objects

Usage

show.BioVector(object)
"show"(object)
"show"(object)
"show"(object)
"show"(object)
"show"(object)
"show"(object)
"show"(object)
"show"(object)
"show"(object)
"show"(object)
"show"(object)
"show"(object)
"show"(object)

Arguments

object

object of class BioVector, PredictionProfile, SpectrumKernel, MismatchKernel, GappyPairKernel, MotifKernel, SymmetricPairKernel, ExplicitRepresentation, ExplicitRepresentationSparse, PredictionProfile, CrossValidationResult, ModelSelectionResult, SVMInformation or KBModel to be displayed

Value

show: show returns an invisible NULL

Details

show displays on overview of the selected object.

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 (accepted). DOI: 10.1093/bioinformatics/btv176.

Examples

## load coiled coil data
data(CCoil)

## show amino acid sequences
ccseq

## define spectrum kernel object
specK1 <- spectrumKernel(k=1, normalized=FALSE)

## show kernel object
show(specK1)

## compute explicit representation for the first 5 sequences
## in dense format
er <- getExRep(ccseq, specK1, sel=1:5, sparse=FALSE)

## show dense explicit representation
show(er)