ExplicitRepresentation {kebabs} | R Documentation

## Explicit Representation Dense and Sparse Classes

### Description

Explicit Representation Dense and Sparse Classes

### Details

In KeBABS this class is the virtual parent class for explicit representations generated from a set of biological sequences for a given kernel. The derived classes `ExplicitRepresentationDense` and `ExplicitRepresentationSparse` are meant to hold explicit representations in dense or sparse format. The kernel used to generate the explicit representation is stored together with the data.

Instances of this class are used for storing explicit representations in dense matrix format. This class is derived from `ExplicitRepresentation`.

Instances of this class are used for storing explicit representations in sparse `dgRMatrix` format. This class is derived from `ExplicitRepresentation`.

### Slots

`usedKernel`

  kernel used for generating the explicit representation

`quadratic`

  boolean indicating a quadratic explicit representation

### Author(s)

Johannes Palme <kebabs@bioinf.jku.at>

### 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.

[Package kebabs version 1.16.0 Index]