Intensity-class: (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure"...

In Bioconductor/ShortRead: FASTQ input and manipulation

(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 <[e-mail]>

See Also

readIntensities

Examples

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

Bioconductor/ShortRead documentation built on Nov. 2, 2024, 4:38 p.m.