RtaIntensity-class {ShortRead} | R Documentation

## (Legacy) Class "RtaIntensity"

### Description

Subclass of `Intensity` for representing image intensity data from the Illumina RTA pipeline.

### Objects from the Class

Objects can be created by calls to `RtaIntensity` or more usually `readIntensities`.

### Slots

Object of `RtaIntensity` have slots:

`readInfo`:

  Object of class `"RtaIntensityInfo"` representing information about each read.

`intensity`:

  Object of class `"ArrayIntensity"` containing an array of intensities with dimensions read, base, and cycle. Nucleotide are A, C, G, T for each cycle.

`measurementError`:

  Object of class `"ArrayIntensity"` containing measurement errors for each read, cycle, and base, with dimensions like that for `intensity`.

`.hasMeasurementError`:

  Object of class `"ScalarLogical"` used internally to indicate whether measurement error information is included.

### Extends

Class `"SolexaIntensity"`, directly.

Class `"Intensity"`, by class "SolexaIntensity", distance 2.

Class `".ShortReadBase"`, by class "SolexaIntensity", distance 3.

### Methods

Class "RtaIntensity" inherits accessor, subsetting, and display methods from class `SolexaIntensity`.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### See Also

`SolexaIntensity`, `readIntensities`

### Examples

    showClass("RtaIntensity")
    showMethods(class="RtaIntensity", where=getNamespace("ShortRead"))

[Package ShortRead version 1.45.4 Index]