RtaIntensity-class: (Legacy) Class "RtaIntensity"

In ShortRead: FASTQ input and manipulation

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 <[e-mail]>

See Also

SolexaIntensity, readIntensities

Examples

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

ShortRead documentation built on Nov. 8, 2020, 8:02 p.m.