ShortReadQ-class {ShortRead}R Documentation

"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 the result of readFastq, or can be constructed from DNAStringSet, QualityScore, and BStringSet objects, as described below.

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

Constructors include:

ShortReadQ
signature(sread = "DNAStringSet", quality = "QualityScore", id = "BStringSet"): Create a ShortReadQ object from reads, their quality scores, and identifiers. The length of id and qualitymust match that of sread.
ShortReadQ
signature(sread = "DNAStringSet", quality = "QualityScore", id = "missing"): Create a ShortReadQ object from reads and their quality scores, creating empty identifiers.
ShortReadQ
signature(sread = "missing", quality = "missing", id = "missing", ...): Create an empty ShortReadQ object.

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

writeFastq
signature(object = "ShortReadQ", file = "character", mode="character", ...): Write object to file in fastq format. mode defaults to ‘w’. This creates a new file, or fails if file already exists. Use mode="a" to append to an existing file. file is expanded using path.expand.
[
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.
append
signature(x = "ShortReadQ", values = "ShortRead", length = "missing"): append the sread, quality and id slots of values after the corresponding fields of x.
narrow
signature(x = "ShortReadQ", start = NA, end = NA, width = NA, use.names = TRUE): ‘narrow’ sread and qualilty so that sequences are between start and end bases, according to narrow in the IRanges package.
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)

[Package ShortRead version 1.2.1 Index]