Container for storing total copy number estimates and confidence
scores of the copy number estimates.
Objects from the Class
Objects can be created by calls of the form new("CopyNumberSet", assayData, phenoData, featureData, experimentData, annotation, protocolData, copyNumber, cnConfidence, ...).
Slots
assayData:
Object of class "AssayData" ~~
phenoData:
Object of class "AnnotatedDataFrame" ~~
featureData:
Object of class "AnnotatedDataFrame" ~~
experimentData:
Object of class "MIAxE" ~~
annotation:
Object of class "character" ~~
protocolData:
Object of class "AnnotatedDataFrame" ~~
.__classVersion__:
Object of class "Versions" ~~
Extends
Class "eSet", directly.
Class "VersionedBiobase", by class "eSet", distance 2.
Class "Versioned", by class "eSet", distance 3.
Methods
cnConfidence
signature(object = "CopyNumberSet"): ...
cnConfidence<-
signature(object = "CopyNumberSet", value = "matrix"): ...
coerce
signature(from = "CNSet", to = "CopyNumberSet"): ...
copyNumber
signature(object = "CopyNumberSet"): ...
copyNumber<-
signature(object = "CopyNumberSet", value = "matrix"): ...
initialize
signature(.Object = "CopyNumberSet"): ...
Note
This container is primarily for platforms for which genotypes are
unavailable. As oligoSnpSet extends this class, methods
related to total copy number that do not depend on genotypes can be
defined at this level.
Author(s)
R. Scharpf
See Also
For genotyping platforms, total copy number estimates and genotype
calls can be stored in the oligoSnpSet class.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(oligoClasses)
Welcome to oligoClasses version 1.34.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/oligoClasses/CopyNumberSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CopyNumberSet-class
> ### Title: Class '"CopyNumberSet"'
> ### Aliases: CopyNumberSet-class CopyNumberSet
> ### cnConfidence,CopyNumberSet-method
> ### cnConfidence<-,CopyNumberSet,matrix-method
> ### copyNumber,CopyNumberSet-method
> ### copyNumber<-,CopyNumberSet,matrix-method
> ### initialize,CopyNumberSet-method checkOrder,CopyNumberSet-method
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("CopyNumberSet")
Class "CopyNumberSet" [package "oligoClasses"]
Slots:
Name: genome assayData phenoData
Class: character AssayData AnnotatedDataFrame
Name: featureData experimentData annotation
Class: AnnotatedDataFrame MIAxE character
Name: protocolData .__classVersion__
Class: AnnotatedDataFrame Versions
Extends:
Class "gSet", directly
Class "eSet", by class "gSet", distance 2
Class "VersionedBiobase", by class "gSet", distance 3
Class "Versioned", by class "gSet", distance 4
> cnset <- new("CopyNumberSet")
> ls(Biobase::assayData(cnset))
[1] "cnConfidence" "copyNumber"
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.