Class "MethyLumiQC" for holding Illumina methylation QC data

This class inherits from the MethyLumi class (and therefore, from eSet in Biobase) and is designed to hold QC data from Illumina Beadstudio output. These data can be potentially useful when determining the cause for quality problems.

Objects from the Class

Objects can be created by calls of the form new("MethyLumiQC", assayData, phenoData, featureData, experimentData, annotation, betas).

Slots

assayData:: Object of class "AssayData"
phenoData:: Object of class "AnnotatedDataFrame"
featureData:: Object of class "AnnotatedDataFrame" containing the annotation columns from the Illumina Beadstudio output. In particular, the names of the probes describe the types of control probes.
experimentData:: Object of class "MIAME"
annotation:: Object of class "character", not currently used
.__classVersion__:: Object of class "Versions"

Extends

Class "MethyLumi", directly. Class "eSet", by class "MethyLumi", distance 2. Class "VersionedBiobase", by class "MethyLumi", distance 3. Class "Versioned", by class "MethyLumi", distance 4.

Methods

initialize: signature(.Object = "MethyLumiQC")
Cy3.N: signature(object = "MethyLumiQC"): ...
Cy3<-: signature(object = "MethyLumiQC", value = "matrix"): ...
Cy5.N: signature(object = "MethyLumiQC"): ...
Cy5<-: signature(object = "MethyLumiQC", value = "matrix"): ...
QCdata<-: signature(object = "MethyLumiSet", value = "MethyLumiQC"): ...
combine: signature(x = "MethyLumiQC", y = "MethyLumiQC"): ...
controlData<-: signature(object = "MethyLumiSet", value = "MethyLumiQC"): ...
controlTypes: signature(object = "MethyLumiQC"): determine the character vector of control types from the QCdata information
hist: signature(x = "MethyLumiQC"): ...
intensitiesByChannel: signature(object = "MethyLumiQC"): ...
methylated: signature(object = "MethyLumiQC"): ...
negctls.stderr: signature(object = "MethyLumiQC", channel = "character"): ...
negctls.stderr: signature(object = "MethyLumiQC", channel = "missing"): ...
negctls: signature(object = "MethyLumiQC", channel = "character"): ...
negctls: signature(object = "MethyLumiQC", channel = "missing"): ...
negnorm: signature(object = "MethyLumiQC", channel = "character"): ...
negnorm: signature(object = "MethyLumiQC", channel = "missing"): ...
normctls: signature(object = "MethyLumiQC"): ...
qcplot: signature(object = "MethyLumiQC", what, ...): QC plots of various controltypes
unmethylated: signature(object = "MethyLumiQC"): ...

Author

Sean Davis <sdavis2@mail.nih.gov>

Examples

showClass("MethyLumiQC")
#> Class "MethyLumiQC" [package "methylumi"]
#> 
#> Slots:
#>                                                                
#> Name:           assayData          phenoData        featureData
#> Class:          AssayData AnnotatedDataFrame AnnotatedDataFrame
#>                                                                
#> Name:      experimentData         annotation       protocolData
#> Class:              MIAxE          character AnnotatedDataFrame
#>                          
#> Name:   .__classVersion__
#> Class:           Versions
#> 
#> Extends: 
#> Class "MethyLumi", directly
#> Class "QCDataOrNULL", directly
#> Class "eSet", by class "MethyLumi", distance 2
#> Class "methylData", by class "MethyLumi", distance 2
#> Class "VersionedBiobase", by class "MethyLumi", distance 3
#> Class "Versioned", by class "MethyLumi", distance 4

Class `"MethyLumiQC"` for holding Illumina methylation QC data