MethyLumiM-class: Class "MethyLumiM": for Illumina Methylation microarray data...

In seandavi/methylumi: Handle Illumina methylation data

Description

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"

Author(s)

Pan DU

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'

See Also

MethyLumi-class and MethyLumiSet-class

Examples

showClass("MethyLumiM")

seandavi/methylumi documentation built on Oct. 28, 2021, 12:42 a.m.