kebabs (version 1.6.2)

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)
## S3 method for class 'PredictionProfile':
show(object)
## S3 method for class 'SpectrumKernel':
show(object)
## S3 method for class 'MismatchKernel':
show(object)
## S3 method for class 'MotifKernel':
show(object)
## S3 method for class 'GappyPairKernel':
show(object)
## S3 method for class 'SymmetricPairKernel':
show(object)
## S3 method for class 'ExplicitRepresentationDense':
show(object)
## S3 method for class 'ExplicitRepresentationSparse':
show(object)
## S3 method for class 'CrossValidationResult':
show(object)
## S3 method for class 'ModelSelectionResult':
show(object)
## S3 method for class 'SVMInformation':
show(object)
## S3 method for class 'KBModel':
show(object)
## S3 method for class '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

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, 31(15):2574-2576, 2015. DOI: http://dx.doi.org/10.1093/bioinformatics/btv176{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)