"ShortReadQ" class for short reads and their quality scores

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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"):

ShortReadQ

signature(sread = "DNAStringSet", quality = "BStringSet", id = "BStringSet"):

Create a ShortReadQ object from reads, their quality scores, and identifiers. When quality is of class BStringSet, the type of encoded quality score is inferred from the letters used in the scores. The length of id and quality must match that of sread.

ShortReadQ

signature(sread = "DNAStringSet", quality = "QualityScore", id = "missing"):

ShortReadQ

signature(sread = "DNAStringSet", quality = "BStringSet", id = "missing"):

Create a ShortReadQ object from reads and their quality scores, creating empty identifiers. When quality is of class BStringSet, the type of encoded quality score is inferred from the letters used in the scores.

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:

quality

inherited from signature(object = "ANY"): access the quality slot of object.

coerce

signature(from = "SFastqQuality", to = "QualityScaledDNAStringSet"):

(Use as(from, "QualityScaledDNAStringSet")) coerce objects of class from to class to, using the quality encoding implied by quality(from). See QualityScore for supported quality classes and their coerced counterparts.

writeFastq

signature(object = "ShortReadQ", file = "character", ...):

writeFastq

signature(object = "ShortReadQ", file = "FastqFile", ...): Write object to file in fastq format. See ?writeFastq for additional arguments mode and full.

[

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.

[<-

signature(x = "ShortReadQ", i = "ANY", j = "missing", ..., y="ShortReadQ"): This method updates x so that records indexed by i are replaced by corresponding records in value.

append

signature(x = "ShortReadQ", values = "ShortRead"): append the sread, quality and id slots of values after the corresponding fields of x.

reverse, reverseComplement

signature(x = "ShortReadQ", ...: reverse or reverse complement the DNA sequence, and reverse the quality sequence.

narrow

signature(x = "ShortReadQ", start = NA, end = NA, width = NA, use.names = TRUE): narrow sread and quality so that sequences are between start and end bases, according to narrow in the IRanges package.

trimTailw

signature(object="ShortReadQ", k="integer", a="character", halfwidth="integer", ..., ranges=FALSE): trim trailing nucleotides when a window of width 2 * halfwidth + 1 contains k or more quality scores falling at or below a.

trimTails

signature(object="ShortReadQ", k="integer", a="character", successive=FALSE, ..., ranges=FALSE): trim trailing nucleotides if k nucleotides fall below the quality encoded by a. If successive=FALSE, the k'th failing nucleotide and all subseqent nucleotides are trimmed. If successive=TRUE, failing nucleotides must occur successively; the sequence is trimmed from the first of the successive failing nucleotides.

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.

qa

signature(dirPath = "ShortReadQ", lane="character", ..., verbose=FALSE): Perform quality assessment on the ShortReadQ object using lane to identify the object and returning an instance of ShortReadQQA. See qa

detail

signature(x = "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

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

sp <- SolexaPath(system.file('extdata', package='ShortRead'))
rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt")
quality(rfq)
sread(reverseComplement(rfq))
quality(reverseComplement(rfq))
quality(trimTails(rfq, 2, "H", successive=TRUE))

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