QualityScore-class: Quality scores for short reads and their alignments

In ShortRead: FASTQ input and manipulation

Description

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

Objects from the class are created using constructors (e.g., NumericQuality) named after the class name.

Defined classes are as follows:

QualityScore

Virtual base class; instances cannot be instantiated.

NumericQuality

A single numeric vector, where values represent quality scores on an arbitrary scale.

IntegerQuality

A integer numeric vector, where values represent quality scores on an arbitrary scale.

MatrixQuality

A rectangular matrix of quality scores, with rows representing reads and columns cycles. The content and interpretation of row and column entries is arbitrary; the rectangular nature implies quality scores from equal-length reads.

FastqQuality

‘fastq’ encoded quality scores stored in a BStringSet instance. Base qualities of a single read are represented as an ASCII character string. The integer-valued quality score of a single base is encoded as its ASCII equivalent plus 33. The precise definition of the integer-valued quality score is unspecified, but is usually a Phred score; the meaning can be determined from the source of the quality scores. Multiple reads are stored as a BStringSet, and so can be of varying lengths.

SolexaQuality

As with FastqQuality, but with integer qualities encoded as ASCII equivalent plus 64.

Extends

Class ".ShortReadBase", directly.

Methods

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 ith read.

[[

signature(x = "MatrixQuality", i = "ANY", j = "ANY"):

Returns the vector of quality scores associated with the ith read.

dim

signature(x = "MatrixQuality"):

The integer(2) dimension (e.g., number of reads, read width) represented by the quality score.

length

signature(x = "QualityScore"):

length

signature(x = "MatrixQuality"):

The integer(1) length (e.g., number of reads) represented by the quality score. Note that length of MatrixQuailty is the number of rows of the corresponding matrix, and not the length of the corresponding numeric vector.

append

signature(x = "QualityScore", values = "QualityScore"): append values after x.

width

signature(x = "QualityScore"):

width

signature(x = "NumericQuality"):

width

signature(x = "MatrixQuality"):

width

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.

show

signature(object = "QualityScore"):

show

signature(object = "NumericQuality"):

show

signature(object = "FastqQuality"):

provide a brief summary of the object content.

detail

signature(x = "QualityScore"):

provide a more detailed view of object content.

The following methods are defined on specific classes:

alphabet

signature(x = "FastqQuality", ...): Return a character vector of valid quality characters.

encoding

signature(x = "FastqQuality", ...), signature(x = "SFastqQuality", ...): Returns a named character vector of integer encodings.

alphabetFrequency

signature(stringSet = "FastqQuality"):

Apply alphabetFrequency to quality scores, returning a matrix as described in alphabetFrequency.

alphabetByCycle

signature(stringSet = "FastqQuality"):

Apply alphabetByCycle to quality scores, returning a matrix as described in alphabetByCycle.

alphabetScore

signature(object = "FastqQuality"):

alphabetScore

signature(object = "SFastqQuality"):

alphabetScore

signature(object = "PhredQuality"):

Apply alphabetScore (i.e., summed base quality, per read) to object.

coerce

signature(from = "FastqQuality", to = "numeric"):

coerce

signature(from = "FastqQuality", to = "matrix"):

coerce

signature(from = "FastqQuality", to = "PhredQuality"):

coerce

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

coerce

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

Use as(from, "matrix")) and similar to coerce objects of class from to class to, using the quality encoding implied by the class. When to is “matrix”, the result is a matrix of type integer with number of columns equal to the maximum width of from; elements i, j with j > width(from)[i] have value NA_integer_. The result always represents the integer encoding of the corresponding quality string.

reverse

signature(x = "FastqQuality", ...: reverse the quality sequence.

narrow

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

trimTailw

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

srorder

signature(x = "FastqQuality"):

srrank

signature(x = "FastqQuality"):

srduplicated

signature(x = "FastqQuality"):

Apply srsort, srorder, srrank, and srduplicated to quality scores, returning objects as described on the appropriate help page.

Integer representations of SFastqQuality and FastqQuality can be obtained with as(x, "matrix").

Author(s)

Martin Morgan <[e-mail]>

See Also

NumericQuality and other constructors.

Examples

names(slot(getClass("QualityScore"), "subclasses"))
encoding(FastqQuality())
encoding(SFastqQuality())

ShortRead documentation built on Nov. 8, 2020, 8:02 p.m.