Intensity-class {ShortRead} | R Documentation

## (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities

### Description

The `Intensity`, `IntensityMeasure`, and `IntensityInfo` classes represent and manipulate image intensity measures. Instances from the class may also contain information about measurement errors, and additional information about the reads from which the intensities are derived.

`Intensity`, and `IntensityMeasure`, are virtual classes, and cannot be created directly. Classes derived from `IntensityMeasure` (e.g., `ArrayIntensity`) and `Intensity` (e.g., `SolexaIntensity`) are used to represent specific technologies.

### Objects from the Class

`ArrayIntensity` objects can be created with calls of the form `ArrayIntensity(array(0, c(1,2,3)))`.

Objects of derived classes can be created from calls such as the `SolexaIntensity` constructor, or more typically by parsing appropriate files (e.g., `readIntensities`).

### Slots

Class `Intensity` has slots:

`readInfo`:

  Object of class `"IntensityInfo"` containing columns for the lane, tile, x, and y coordinates of the read.

`intensity`:

  Object of class `"IntensityMeasure"` containing image intensity data for each read and cycle.

`measurementError`:

  Object of class `"IntensityMeasure"` containing measures of image intensity uncertainty for each read and cycle.

`.hasMeasurementError`:

  Length 1 logical variable indicating whether intensity standard errors are included (internal use only).

Classes `IntensityInfo` and `IntensityMeasure` are virtual classes, and have no slots.

### Extends

These classes extend `".ShortReadBase"`, directly.

### Methods

Methods and accessor functions for `Intensity` include:

readIntensityInfo

  `signature(object = "Intensity")`: access the `readInfo` slot of `object`.

intensity

  `signature(object = "Intensity")`: access the `intensity` slot of `object`.

measurementError

  `signature(object = "Intensity")`: access the `nse` slot of `object`, or signal an error if no standard errors are available.

dim

  `signature(object = "Intensity")`: return the dimensions (e.g., number of reads by number of cycles) represented by `object`.

show

  `signature(object = "Intensity")`: provide a compact representation of the object.

Subsetting `"["` is available for the `IntensityMeasure` class; the `drop` argument to `"["` is ignored.

Subsetting with `"[["` is available for the `ArrayIntensity` class. The method accepts three arguments, corresponding to the read, base, and cycle(s) to be selected. The return value is the array (i.e., underlying data values) corresponding to the selected indices.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### See Also

`readIntensities`

### Examples

    showMethods(class="Intensity", where=getNamespace("ShortRead"))
    example(readIntensities)

[Package ShortRead version 1.38.0 Index]