BioVector-class {kebabs} | R Documentation

## BioVector, DNAVector, RNAVector and AAVector Classes

### Description

BioVector, DNAVector, RNAVector and AAVector Classes

### 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.

### 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".

### 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 1.20.0 Index]