QualityScore: Construct objects indicating read or alignment quality

Description Usage Arguments Value Author(s) See Also Examples

Description

Use these functions to construct quality indicators for reads or alignments. See QualityScore for details of object content and methods available for manipulating them.

Usage

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NumericQuality(quality = numeric(0))
IntegerQuality(quality = integer(0))
MatrixQuality(quality = new("matrix"))
FastqQuality(quality, ...)
SFastqQuality(quality, ...)

Arguments

quality

An object used to initialize the data structure. Appropriate objects are indicated in the constructors above for Numeric, Integer, and Matrix qualities. For FastqQuality and SFastqQuality, methods are defined for BStringSet, character, and missing.

...

Additional arguments, currently unused.

Value

Constructors return objects of the corresponding class derived from QualityScore.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

See Also

QualityScore, readFastq, readAligned

Examples

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nq <- NumericQuality(rnorm(20))
nq
quality(nq)
quality(nq[10:1])

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