ExplicitRepresentation-class: Explicit Representation Dense and Sparse Classes

Description Details Slots Author(s) References

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 <[email protected]>

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.


kebabs documentation built on May 31, 2017, 11:07 a.m.