DnaSeq-class: Class "DnaSeq" and "RnaSeq"

In sequences: Generic and Biological Sequences

Description

The DnaSeq and RnaSeq are instances of the virtual GenericSeq class for "DNA" and "RNA" respectively. Their alphabets are defined accordingly.

Objects from the Class

Instance of DnaSeq and RnaSeq can be created by reading fasta files using the readFasta function.

Slots

See the GenericSeq class for details about the generic slots and methods.

Extends

Class GenericSeq, directly.

Methods

See GenericSeq for inherited methods.

comp

signature(object = "DnaSeq"): return the complement of the sequence string of the sequence instance.

transcribe

signature(object = "DnaSeq"): transcribes the DnaSeq instance into a RnaSeq instance.

Author(s)

Laurent Gatto <[e-mail]>

See Also

See also the GenericSeq virutal class.

Examples

data("dnaseq")
dnaseq
rnaseq <- transcribe(dnaseq)
rnaseq

Example output

Loading required package: Rcpp
This is package 'sequences'

Object of class DnaSeq 
 Id: example dna sequence 
 Length: 132 
 Alphabet: A C G T 
 Sequence: AGCATACGACGACTACGACACTACGACATCAGACACTACAGACTACTACGACTACAGACATCAGACACTACATATTTACATCATCAGAGATTATATTAACATCAGACATCGACACATCATCATCAGCATCAT 
Object of class RnaSeq 
 Id: example dna sequence -- transcribed 
 Length: 132 
 Alphabet: A C G U 
 Sequence: AGCAUACGACGACUACGACACUACGACAUCAGACACUACAGACUACUACGACUACAGACAUCAGACACUACAUAUUUACAUCAUCAGAGAUUAUAUUAACAUCAGACAUCGACACAUCAUCAUCAGCAUCAU 

sequences documentation built on May 2, 2019, 6:45 a.m.