MethyLumi-class {methylumi} | R Documentation

## The base class for storing Illumina Methylation data

### Description

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"`

: Find the unique control type beeds in the QCdata slot.

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",...)`

: summary method for MethyLumi objects.

### Author(s)

Sean Davis <sdavis2@mail.nih.gov>

### See Also

`methylumiR`, `MethyLumiSet`, `MethyLumiQC`, `eSet`

### Examples

    ## The class structure
    showClass("MethyLumi")
    ## 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
    ## Get history information
    getHistory(mldat)
    ## Get QC data, which is another eSet-derived object
    QCdata(mldat)

[Package methylumi version 2.26.0 Index]