SolexaIntensity-class: Classes "SolexaIntensity" and "SolexaIntensityInfo"

In ShortRead: FASTQ input and manipulation

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 <[e-mail]>

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

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