| ShortReadQ-class {ShortRead} | R Documentation |
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 this class are the result of readFastq, or
can be constructed from DNAStringSet, QualityScore, and
BStringSet objects, as described below.
Slots 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).
Class "ShortRead", directly.
Class ".ShortReadBase", by class "ShortRead", distance 2.
Constructors include:
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.signature(sread = "DNAStringSet", quality = "QualityScore", id = "missing"):
Create a ShortReadQ object from reads and their quality
scores, creating empty identifiers.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:
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.signature(x = "ShortReadQ", values = "ShortRead", length = "missing"):
append the sread, quality and id slots of
values after the corresponding fields of x.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.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(object = "ShortReadQ"): display the
first and last entries of each of sread, id, and
quality entries of object.Martin Morgan
readFastq for creation of objects of this class from
fastq-format files.
showClass("ShortReadQ")
showMethods(class="ShortReadQ", inherit=FALSE)
showMethods(class="ShortRead", inherit=FALSE)