The base class for storing Illumina Methylation data

This class inherits from eSet from the Biobase package and is used as a base class for the other two methylumi classes, MethyLumiSet and MethyLumiQC.

Objects from the Class

The MethyLumi class is a virtual class and is not meant to be instantiated. Instead, one should instantiate a MethyLumiSet or a MethyLumiQC object.

Slots

assayData:: Object of class "AssayData"
phenoData:: Object of class "AnnotatedDataFrame"
featureData:: Object of class "AnnotatedDataFrame" that will hold the annotation columns from the Beadstudio output, if they are available.
experimentData:: Object of class "MIAME"
annotation:: Object of class "character"; note that this slot is not currently used, but may be used in the future to store the character name of the annotation package, if available.
.__classVersion__:: Object of class "Versions"

Extends

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

Methods

pvals<-: signature(object = "MethyLumi", value = "matrix"): Set the assayData slot of the same name and stores the P-values from BeadStudio
pvals: signature(object = "MethyLumi"): Get the assayData slot of the same name
betas<-: signature(object = "MethyLumi", value = "matrix"): Set the assayData slot of the same name and represents the methylation values for the samples, analogous to exprs() in gene expression data.
betas: signature(object = "MethyLumi"): Get the assayData slot of the same name
methylated<-: signature(object = "MethyLumi", value = "matrix"): Set the assayData slot that represents the Methylated single-channel signal
methylated: signature(object = "MethyLumi"): Get the assayData slot that represents the Methylated single-channel signal
unmethylated<-: signature(object = "MethyLumi", value = "matrix"): Set the assayData slot that represents the Unmethylated single-channel signal
unmethylated: signature(object = "MethyLumi"): Get the assayData slot that represents the Unmethylated single-channel signal
controlTypes: signature(object = "MethyLumi"
qcplot: signature(object = "MethyLumi",what,...): Plot of QC data. This plot can be useful for diagnosing the problems associated with specific samples or arrays. The value for "what" is one of the control types (which can be found by using controlTypes() on the object.
summary: signature(object = "MethyLumi",...)

Author

Sean Davis <sdavis2@mail.nih.gov>

Examples

## The class structure
showClass("MethyLumi")
#> Class "MethyLumi" [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 "eSet", directly
#> Class "methylData", directly
#> Class "VersionedBiobase", by class "eSet", distance 2
#> Class "Versioned", by class "eSet", distance 3
#> 
#> Known Subclasses: "MethyLumiQC", "MethyLumiSet"
## read in some data
## Read in sample information
samps <- read.table(system.file("extdata/samples.txt",
                                package = "methylumi"),sep="\t",header=TRUE)
## Perform the actual data reading
## This is an example of reading data from a 
## Sentrix Array format file (actually two files,
## one for data and one for QC probes)
mldat <- methylumiR(system.file('extdata/exampledata.samples.txt',
        package='methylumi'),
      qcfile=system.file('extdata/exampledata.controls.txt',
        package="methylumi"),
      sampleDescriptions=samps)
mldat
#> 
#> Object Information:
#> MethyLumiSet (storageMode: lockedEnvironment)
#> assayData: 1536 features, 10 samples 
#>   element names: Avg_NBEADS, BEAD_STDERR, betas, methylated, pvals, unmethylated 
#> protocolData: none
#> phenoData
#>   sampleNames: M_1 M_2 ... F_10 (10 total)
#>   varLabels: sampleID SampleLabel Sample Gender
#>   varMetadata: labelDescription
#> featureData
#>   featureNames: AATK_E63_R AATK_P519_R ... ZP3_P220_F (1536 total)
#>   fvarLabels: TargetID ProbeID ... PRODUCT (17 total)
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation:  
#> Major Operation History:
#>                    submitted                   finished
#> 1 2026-10-16 15:00:53.866097 2026-10-16 15:00:54.075536
#>                                                                                                                                                                                                             command
#> 1 methylumiR(filename = system.file("extdata/exampledata.samples.txt",     package = "methylumi"), qcfile = system.file("extdata/exampledata.controls.txt",     package = "methylumi"), sampleDescriptions = samps)
## Get history information
getHistory(mldat)
#>                    submitted                   finished
#> 1 2026-10-16 15:00:53.866097 2026-10-16 15:00:54.075536
#>                                                                                                                                                                                                             command
#> 1 methylumiR(filename = system.file("extdata/exampledata.samples.txt",     package = "methylumi"), qcfile = system.file("extdata/exampledata.controls.txt",     package = "methylumi"), sampleDescriptions = samps)
## Get QC data, which is another eSet-derived object
QCdata(mldat)
#> MethyLumiQC (storageMode: lockedEnvironment)
#> assayData: 44 features, 10 samples 
#>   element names: Avg_NBEADS, BEAD_STDERR, methylated, pvals, unmethylated 
#> protocolData: none
#> phenoData: none
#> featureData
#>   featureNames: ALLELE SPECIFIC EXTENSION ALLELE SPECIFIC EXTENSION.1
#>     ... SECOND HYBRIDIZATION.5 (44 total)
#>   fvarLabels: TargetID ProbeID
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation: