SolexaIntensity-class {ShortRead} | R Documentation |
Instances of Intensity
and
IntensityInfo
for representing image intensity
data from Solexa experiments.
Objects can be created by calls to SolexaIntensityInfo
or
SolexaIntensity
, or more usually readIntensities
.
Object of SolexaIntensity
have slots:
readInfo
:"SolexaIntensityInfo"
representing information about each read.intensity
:"ArrayIntensity"
containing an array of intensities with dimensions read, base, and
cycle. Nucleotide are A, C, G, T for each cycle.measurementError
:"ArrayIntensity"
containing measurement errors for each
read, cycle, and base, with dimensions like that for
intensity
. .hasMeasurementError
:"ScalarLogical"
used internally to indicate whether
measurement error information is included.
Object of SolexaIntensityInfo
"data.frame"
, inheritted from
AnnotatedDataFrame
."data.frame"
, inheritted
from AnnotatedDataFrame
."character"
, inheritted
from AnnotatedDataFrame
..__classVersion__
"Versions"
,
inheritted from AnnotatedDataFrame
."ScalarLogical"
, used internally
to indicate whether the user initialized this object.
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.
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
.
Martin Morgan <mtmorgan@fhcrc.org>
showClass("SolexaIntensity") sp <- SolexaPath(system.file('extdata', package='ShortRead')) int <- readIntensities(sp) int # SolexaIntensity readInfo(int) # SolexaIntensityInfo int[1:5,,] # read 1:5