SolexaIntensity-class {ShortRead} | R Documentation

## Classes "SolexaIntensity" and "SolexaIntensityInfo"

### Description

Instances of `Intensity` and `IntensityInfo` for representing image intensity data from Solexa experiments.

### Objects from the Class

Objects can be created by calls to `SolexaIntensityInfo` or `SolexaIntensity`, or more usually `readIntensities`.

### Slots

Object of `SolexaIntensity` have slots:

`readInfo`:

  Object of class `"SolexaIntensityInfo"` 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.

Object of `SolexaIntensityInfo`

data

  Object of class `"data.frame"`, inherited from `AnnotatedDataFrame`.

varMetadata

  Object of class `"data.frame"`, inherited from `AnnotatedDataFrame`.

dimLabels

  Object of class `"character"`, inherited from `AnnotatedDataFrame`.

`.__classVersion__`

  Object of class `"Versions"`, inherited from `AnnotatedDataFrame`.

.init

  Object of class `"ScalarLogical"`, used internally to indicate whether the user initialized this object.

### Extends

Class `SolexaIntensity`:

Class `"Intensity"`, directly. Class `".ShortReadBase"`, by class "Intensity", distance 2.

Class `SolexaIntensityInfo`:

Class `"AnnotatedDataFrame"`, directly Class `"IntensityInfo"`, directly Class `"Versioned"`, by class "AnnotatedDataFrame", distance 2 Class `".ShortReadBase"`, by class "IntensityInfo", distance 2 Class `"IntensityInfo"`, directly.

### Methods

Class "SolexaIntensity" inherits accessor and display methods from class `Intensity`. Additional methods include:

`[`

  `signature(x = "SolexaIntensity", i="ANY", j="ANY", k="ANY")`:

  Selects the ith read, jth nucleotide, and kth cycle. Selection is coordinated across intensity, measurement error, and read information.

Class "SolexaIntensityInfo" inherits accessor, subsetting, and display methods from class `IntensityInfo` and `AnnotatedDataFrame`.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### See Also

`readIntensities`

### Examples

    showClass("SolexaIntensity")
    sp <- SolexaPath(system.file('extdata', package='ShortRead'))
    int <- readIntensities(sp)
    int 				# SolexaIntensity
    readIntensityInfo(int)		# SolexaIntensityInfo
    int[1:5,,]			# read 1:5

[Package ShortRead version 1.52.0 Index]