NumericQuality

IntegerQuality

MatrixQuality

FastqQuality

FastqQuality,BStringSet-method

FastqQuality,character-method

FastqQuality,missing-method

SFastqQuality

SFastqQuality,BStringSet-method

SFastqQuality,character-method

SFastqQuality,missing-method

An object used to initialize the data
    structure. Appropriate objects are indicated in the constructors
    above for Numeric, Integer, and Matrix qualities. For
    <code>FastqQuality</code> and <code>SFastqQuality</code>, methods are defined
    for <code><a rd-options="Biostrings:XStringSet-class" href="/link/BStringSet?package=ShortRead&version=1.30.0&to=Biostrings%3AXStringSet-class" data-mini-rdoc="Biostrings:XStringSet-class::BStringSet">BStringSet</a></code>,
    <code>character</code>, and <code>missing</code>.

quality


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


 manip 

QualityScore

This package implements sampling, iteration, and input of
FASTQ files. The package includes functions for filtering and
trimming reads, and for generating a quality assessment report.
Data are represented as DNAStringSet-derived objects, and
easily manipulated for a diversity of purposes.  The package
also contains legacy support for early single-end, ungapped
alignment formats.

Bioconductor Package Maintainer

ShortRead

FASTQ input and manipulation

QualityScore function

An object used to initialize the data
    structure. Appropriate objects are indicated in the constructors
    above for Numeric, Integer, and Matrix qualities. For
    <code>FastqQuality</code> and <code>SFastqQuality</code>, methods are defined
    for <code><a href="BStringSet" rd-options="Biostrings:XStringSet-class">BStringSet</a></code>,
    <code>character</code>, and <code>missing</code>.

Use these functions to construct quality indicators for reads or
  alignments. See <code><linkS4class>QualityScore</linkS4class></code> for details of
  object content and methods available for manipulating them.

QualityScore: Construct objects indicating read or alignment quality

Description

Usage

Arguments

Value

See Also

Examples