MethyLumiM-class {methylumi} | R Documentation

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

### 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")

[Package methylumi version 2.34.0 Index]