QualityScore-class {ShortRead} | R Documentation |
This class hierarchy represents quality scores for short
reads. QualityScore
is a virtual base class, with derived
classes offering different ways of representing qualities. Methods
defined on QualityScore
are implemented in all derived
classes.
Objects from the class are created using constructors (e.g.,
NumericQuality
) named after the class name.
Class ".ShortReadBase"
, directly.
The following methods are defined on all QualityScore
and
derived classes:
signature(x = "QualityScore", i = "ANY", j = "missing")
signature(x = "MatrixQuality", i = "ANY", j = "missing")
:
Subset the object, with index i
indicating the reads for
which quality scores are to be extracted. The class of the result
is the same as the class of x
. It is an error to provide
any argument other than i
.
signature(x = "QualityScore", i = "ANY", j = "ANY")
:
Subset the object, returning the quality score (e.g., numeric
value) of the i
th read.
signature(x = "MatrixQuality", i = "ANY", j = "ANY")
:
Returns the vector of quality scores associated with the
i
th read.
signature(x = "QualityScore")
:signature(x = "MatrixQuality")
:
The numeric(1) length (e.g., number of reads) represented by the quality score.
signature(x = "QualityScore")
:signature(x = "NumericQuality")
:signature(x = "MatrixQuality")
:signature(x = "FastqQuality")
:
A numeric vector with length equal to the number of quality
scores, and value equal to the number of quality scores for each
read. For instance, a FastqQuality
will have widths
equal to the number of nucleotides in the underlying short read.
signature(object = "QualityScore")
:signature(object = "NumericQuality")
:signature(object = "FastqQuality")
:
provide a brief summary of the object content.
signature(object = "QualityScore")
:
provide a more detailed view of object content.
The following methods are defined on specific classes:
signature(x = "FastqQuality")
:
Return a character vector of valid quality characters.
signature(stringSet = "FastqQuality")
:
Apply alphabetFrequency
to quality
scores, returning a matrix as described in
alphabetFrequency
.
signature(stringSet = "FastqQuality")
:
Apply alphabetByCycle
to quality scores, returning a
matrix as described in alphabetByCycle
.
signature(object = "FastqQuality")
:signature(object = "SFastqQuality")
:
Apply alphabetScore
(i.e., summed base quality, per
read) to object
.
signature(x = "FastqQuality")
:signature(x = "FastqQuality")
:signature(x = "FastqQuality")
:signature(x = "FastqQuality")
:
Apply srsort
, srorder
, srrank
, and
srduplicated
to quality scores, returning objects as
described on the appropriate help page.
Martin Morgan <mtmmorgan@fhcrc.org>
NumericQuality
and other constructors.
names(slot(getClass("QualityScore"), "subclasses"))