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
quality
must 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)