BioVector-class: BioVector, DNAVector, RNAVector and AAVector Classes

Description

BioVector, DNAVector, RNAVector and AAVector Classes

Arguments

Slots

NAMES: sequence names
elementMetadata: element metadata, which is applicable per element and holds a DataTable with one entry per sequence in each column. KeBABS uses the column names "annotation" and "offset".
metadata: metadata applicable for the entire sequence set as list. KeBABS stores the annotation character set as list element named "annotationCharset".

Details

This class is the parent class for representing sets of biological sequences with support of lowercase characters. The derived classes DNAVector, RNAVector and AAVector hold DNA-, RNA- or AA-sequences which can contain also lowercase characters. In many cases repeat regions are coded as lowercase characters and with the BioVector based classes sequence analysis with and without repeat regions can be performed from the same sequence set. Whenever lowercase is not needed please use the XStringSet based classes as they provide much richer functionality. The class BioVector is derived from "character" and holds the sequence information as character vector. Interfaces for the small set of functions needed in KeBABS are designed consistent with XStringSet.

Instances of the DNAVector class are used for representing sets of DNA sequences.

Instances of the RNAVector class are used for representing sets of RNA sequences.

Instances of the AAVector class are used for representing sets of amino acid sequences.

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.