This class provides a way to store and manipulate, in a coordinated fashion, the reads, identifiers, and quality scores of uniform-length short reads.
readFastq, or
can be constructed from DNAStringSet, QualityScore, and
BStringSet objects, as described below. sread and id are inherited from
ShortRead. An additional slot defined in this
class is:
quality:"BStringSet"
representing a quality score (see readFastq for some
discussion of quality score)."ShortRead", directly.
Class ".ShortReadBase", by class "ShortRead", distance 2.signature(sread = "DNAStringSet", quality = "QualityScore", id = "BStringSet"):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.signature(sread = "DNAStringSet", quality = "QualityScore", id = "missing"):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. signature(sread = "missing", quality = "missing", id = "missing"):
Create an empty ShortReadQ object.accessors for additional functions to access slot
content, and ShortRead for inherited
methods. Additional methods include: signature(object = "ANY"):
access the quality slot of object.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.signature(object = "ShortReadQ", file =
"character", ...):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.signature(x = "ShortReadQ", values = "ShortRead"):
append the sread, quality and id slots of
values after the corresponding fields of x.signature(x = "ShortReadQ", ...:
reverse or reverse complement the DNA sequence, and reverse the
quality sequence.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.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.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.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".signature(object = "ShortReadQ"):
See alphabetScore for details.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 qasignature(x = "ShortReadQ"): display the
first and last entries of each of sread, id, and
quality entries of object. readFastq for creation of objects of this class from
fastq-format files.
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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