"ShortReadQ" class for short reads and their quality scores

Description

This class provides a way to store and manipulate, in a coordinated fashion, the reads, identifiers, and quality scores of uniform-length short reads.

Objects from the Class

Objects from this class are not normally created directly by the user, but are instead the result of readFastq.

Slots

Slots sread and id are inherited from ShortRead. An additional slot defined in this class is:

quality:

Object of class "BStringSet" representing a quality score (see readFastq for some discussion of quality score).

Extends

Class "ShortRead", directly. Class ".ShortReadBase", by class "ShortRead", distance 2.

Methods

See accessors for additional functions to access slot content, and ShortRead for inherited methods. Additional methods include:

[

signature(x = "ShortReadQ", i = "ANY", j = "missing"): This method creates a new ShortReadQ object containing only those reads indexed by i. Additional methods on ‘[,ShortRead’ do not provide additional functionality, but are present to limit inappropriate use.

alphabetByCycle

signature(stringSet = "ShortReadQ"): Apply alphabetByCycle to the sread component, the quality component, and the combination of these two components of stringSet, returning a list of matrices with three elements: "sread", "quality", and "both".

alphabetScore

signature(object = "ShortReadQ"): See alphabetScore for details.

detail

signature(object = "ShortReadQ"): display the first and last entries of each of sread, id, and quality entries of object.

Author(s)

Martin Morgan

See Also

readFastq for creation of objects of this class from fastq-format files.

Examples

showClass("ShortReadQ")
showMethods(class="ShortReadQ", inherit=FALSE)
showMethods(class="ShortRead", inherit=FALSE)