Class "MethyLumiM": for Illumina Methylation microarray data using logRatios

MethyLumiM is a class inherited from ExpressionSet-class. It is designed for Illumina Methylation microarray data. The exprs dataMatrix included in the assayData slot of MethyLumiM object includes a matrix of M-values, which is the log2 ratio of methylated and unmethylated probe intensities. The MethyLumiM class include a boxplot function uniquely designed for two-mode histogram data. It also include a coerce function to map from MethyLumi-class, MethyLumiSet-class or other eSet-class inherited object to MethyLumiM class object.

Objects from the Class

Objects can be created by calls of the form new("MethyLumiM", exprs, methylated, unmethylated, detection, methylated.N, unmethylated.N, ..., assayData). The "exprs" is a matrix of M-values, which is the log2 ratio of methylated and unmethylated probe intensities; "methylated" and "unmethylated" are intensity matrix measured by methylated and unmethylalted probes of Illumina Infinium methylation microarray; "detection" is the detection p-value outputted by Illumina GenomeStudio software; "methylated.N" and "unmethylated.N" are bead numbers for methylated and unmethylalted probes. "exprs", "methylated" and "unmethylated" information are required for MethyLumiM class. When creating a new MethyLumiM object, the information of "exprs", "methylated", "unmethylated" and "detection" can also be provided directly through "assayData".

Slots

history:: Object of class "data.frame" recording the operation history of the LumiBatch object.
controlData:: Object of class "MethyLumiQC" to keep the QC probe measurement information.
dataType:: The type of data stored in the "exprs" data matrix in "assayData". It can be "M" (M-value), "Beta" (Beta-value") or "Intensity" (Intensity of CpG-site)
assayData:: Object of class "AssayData", which includes "exprs", "methylated", "unmethylated", "detection", "methylated.N" and "unmethylated.N" data matrix
phenoData:: Object of class "AnnotatedDataFrame", See eSet-class
featureData:: Object of class "AnnotatedDataFrame", See eSet-class
experimentData:: Object of class "MIAME", See eSet-class
annotation:: Object of class "character", See eSet-class
protocolData:: Object of class "AnnotatedDataFrame", See eSet-class
.__classVersion__:: Object of class "Versions", See eSet-class

Extends

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

Methods

boxplot: signature(x = "MethyLumiM"): plot distribution of M-value
coerce: signature(from = "eSet", to = "MethyLumiM"): map from MethyLumi-class, MethyLumiSet-class or other eSet-class inherited object to MethyLumiM class object. MethyLumiM object will only keep "exprs", "methylated", "unmethylated" and "detection" data matrix in the assayData.
getHistory: signature(object = "MethyLumiM"): access the operation history of MethyLumiM object.
initialize: signature(.Object = "MethyLumiM"): class initialization
methylated: signature(object = "MethyLumiM"): retrieve the data matrix measured by methylated probes
methylated<-: signature(object = "MethyLumiM"): set the data matrix measured by methylated probes
unmethylated: signature(object = "MethyLumiM"): retrieve the data matrix measured by unmethylated probes
unmethylated<-: signature(object = "MethyLumiM"): set the data matrix measured by unmethylated probes
methylated.N: signature(object = "MethyLumiM"): retrieve the data matrix keeping the number of beads of methylated probes
methylated.N<-: signature(object = "MethyLumiM"): set the data matrix keeping the number of beads of methylated probes
unmethylated.N: signature(object = "MethyLumiM"): retrieve the data matrix keeping the number of beads of unmethylated probes
unmethylated.N<-: signature(object = "MethyLumiM"): set the data matrix keeping the number of beads of unmethylated probes
detection: signature(object = "MethyLumiM"): retrieve detection data matrix in AssayData-class
detection<-: signature(object = "MethyLumiM"): set detection data matrix in AssayData-class
controlData: signature(object = "MethyLumiM"): retrieve the controlData in MethyLumiQC-class
controlData<-: signature(object = "MethyLumiM"): set controlData in MethyLumiQC-class
dataType: signature(object = "MethyLumiM"): retrieve the dataType, by default it is "M", it can also be "Beta" or "Intensity"
dataType<-: signature(object = "MethyLumiM"): set dataType in MethyLumiM-class, the value can be "M", "Beta" or "Intensity"

References

1. Du, P., Zhang, X, Huang, C.C., Jafari, N., Kibbe, W.A., Hou, L., and Lin, S.M., (2010) 'Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis'

Author

Pan DU

Examples

showClass("MethyLumiM")
#> Class "MethyLumiM" [package "methylumi"]
#> 
#> Slots:
#>                                                                
#> Name:         controlData            history           dataType
#> Class:       QCDataOrNULL         data.frame          character
#>                                                                
#> Name:      experimentData          assayData          phenoData
#> Class:              MIAME          AssayData AnnotatedDataFrame
#>                                                                
#> Name:         featureData         annotation       protocolData
#> Class: AnnotatedDataFrame          character AnnotatedDataFrame
#>                          
#> Name:   .__classVersion__
#> Class:           Versions
#> 
#> Extends: 
#> Class "ExpressionSet", directly
#> Class "methylData", directly
#> Class "eSet", by class "ExpressionSet", distance 2
#> Class "VersionedBiobase", by class "ExpressionSet", distance 3
#> Class "Versioned", by class "ExpressionSet", distance 4