show-methods: Display Various KeBABS Objects

In kebabs: Kernel-Based Analysis Of Biological Sequences

Description

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

Usage

show.BioVector(object)

## S4 method for signature 'PredictionProfile'
show(object)

## S4 method for signature 'SpectrumKernel'
show(object)

## S4 method for signature 'MismatchKernel'
show(object)

## S4 method for signature 'MotifKernel'
show(object)

## S4 method for signature 'GappyPairKernel'
show(object)

## S4 method for signature 'SymmetricPairKernel'
show(object)

## S4 method for signature 'ExplicitRepresentationDense'
show(object)

## S4 method for signature 'ExplicitRepresentationSparse'
show(object)

## S4 method for signature 'CrossValidationResult'
show(object)

## S4 method for signature 'ModelSelectionResult'
show(object)

## S4 method for signature 'SVMInformation'
show(object)

## S4 method for signature 'KBModel'
show(object)

## S4 method for signature 'ROCData'
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

Details

show displays on overview of the selected object.

Value

show: show returns an invisible NULL

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.

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)

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