RtaIntensity-class

Subclass of <code>Intensity</code> for representing image
 intensity data from the Illumina RTA pipeline.

classes

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

RtaIntensity-class function

Objects can be created by calls to <code>RtaIntensity</code> or more usually
 <code>readIntensities</code>.

Objects from the Class

Object of <code>RtaIntensity</code> have slots: <dl> <dt><code>readInfo</code>:</dt><dd>Object of class <code>"RtaIntensityInfo"</code>
 representing information about each read.</dd> <dt><code>intensity</code>:</dt><dd>Object of class <code>"ArrayIntensity"</code>
 containing an array of intensities with dimensions read, base, and
 cycle. Nucleotide are A, C, G, T for each cycle.</dd> <dt><code>measurementError</code>:</dt><dd>Object of class
 <code>"ArrayIntensity"</code> containing measurement errors for each
 read, cycle, and base, with dimensions like that for
 <code>intensity</code>. </dd> <dt><code>.hasMeasurementError</code>:</dt><dd>Object of class
 <code>"ScalarLogical"</code> used internally to indicate whether
 measurement error information is included.</dd> </dl>

Slots

Class <code>"SolexaIntensity"</code>, directly. Class <code>"Intensity"</code>, by class "SolexaIntensity", distance 2. Class <code>".ShortReadBase"</code>, by class "SolexaIntensity", distance 3.

Extends

Class "RtaIntensity" inherits accessor, subsetting, and display
 methods from class <code>SolexaIntensity</code>.

Methods

Subclass of <code><linkS4class>Intensity</linkS4class></code> for representing image
 intensity data from the Illumina RTA pipeline.

RtaIntensity-class: (Legacy) Class "RtaIntensity"

Description

Arguments

Objects from the Class

Slots

Extends

Methods

See Also

Examples