MethyLumiSet-class {methylumi} | R Documentation

## Class `"MethyLumiSet"` for containing Illumina methylation data

### Description

This class inherits from the MethyLumi class (and therefore, from eSet in Biobase) and is designed to hold both the intensities and the calculated betas, as well as pvalues if present.

### Objects from the Class

Objects can be created by calls of the form `new("MethyLumiSet", assayData, phenoData, featureData, experimentData, annotation, betas)`. An object of this type is the main storage class for methylation data from Illumina. Subsetting, etc., works as normal (rows represent genes, columns represent samples). There is also a rudimentary history tracking system that is modeled after that from the lumi package.

### Slots

`QC`:

  Object of class `"QCDataOrNULL"`, containing either the `MethyLumiQC` object or NULL

`history`:

  Object of class `"data.frame"`, containing a running history of transforms to the data contained herein

`assayData`:

  Object of class `AssayData`

`phenoData`:

  Object of class `AnnotatedDataFrame`

`featureData`:

  Object of class `AnnotatedDataFrame`, containing the annotation columns from the Illumina Beadstudio output

`experimentData`:

  Object of class `MIAME`

`annotation`:

  Object of class `"character"`, not currently used

`.__classVersion__`:

  Object of class `"Versions"`

`protocolData`:

  Object of class `"AnnotatedDataFrame"` that contains protocol information, including scan date if available

### Extends

Class `"MethyLumi"`, directly. Class `"methylData"`, directly. Class `"eSet"`, by class "MethyLumi", distance 2. Class `"VersionedBiobase"`, by class "MethyLumi", distance 3. Class `"Versioned"`, by class "MethyLumi", distance 4.

### Methods

[

  `signature(x = "MethyLumiSet")`: subsetting, genes as rows, samples as columns

betas<-

  `signature(object = "MethyLumiSet", value = "matrix")`: Set the assayData slot of the same name

betas

  `signature(object = "MethyLumiSet")`: Get the assayData slot of the same name

boxplot

  `signature(x = "MethyLumiSet")`: boxplot of all sample betas

combine

  `signature(x = "MethyLumiSet", y = "MethyLumiSet")`

corplot

  `signature(x = "MethyLumiSet")`

exprs

  `signature(object = "MethyLumiSet")`: returns m-values

getHistory

  `signature(object = "MethyLumiSet")`: returns a data.frame containing the history for this object

hist

  `signature(x = "MethyLumiSet")`: histogram of the betas for the data

initialize

  `signature(.Object = "MethyLumiSet")`

pairs

  `signature(x = "MethyLumiSet")`: pairs plot of the betas for the object. Note that pairs plots of more than a few samples are not very useful.

plotSampleIntensities

  `signature(x = "MethyLumiSet")`: The intensities as output by the Beadstudio software often show a considerable amount of dye bias. This method shows a graphical example of this dye bias. In short, for each of the Cy3 and Cy5 channels, a cutoff in beta is used to calculate which Cy3 and Cy5 values should be plotted at high-methylation and low-methylation status. Any offset between Cy3 and Cy5 when plotted in this way likely represents dye bias and will lead to biases in the estimate of beta.

QCdata<-

  `signature(object = "MethyLumiSet", value = "MethyLumiQC")`: assign QC data to the QC slot

QCdata

  `signature(object = "MethyLumiSet")`: retrieve the QC data.

show

  `signature(object = "MethyLumiSet")`

methylated<-

  `signature(object = "MethyLumiSet", value = "matrix")`: Set the assayData slot associated with methylated intensity

methylated

  `signature(object = "MethyLumiSet")`: Get the assayData slot associated with methylated intensity

unmethylated<-

  `signature(object = "MethyLumiSet", value = "matrix")`: Set the assayData slot associated with unmethylated intensity

unmethylated

  `signature(object = "MethyLumiSet")`: Get the assayData slot associated with unmethylated intensity

qcplot

  `signature(object = "MethyLumiSet", what, ...)`: QC plots of various controltypes

controlTypes

  `signature(object = "MethyLumiSet")`: determine the character vector of control types from the QCdata information

Cy3.N

  `signature(object = "MethyLumiSet")`: ...

Cy5.N

  `signature(object = "MethyLumiSet")`: ...

combine27k450k

  `signature(x = "MethyLumiSet", y = "MethyLumiSet")`: ...

controlData

  `signature(object = "MethyLumiSet")`: ...

controlData<-

  `signature(object = "MethyLumiSet", value = "MethyLumiQC")`: ...

featureFilter

  `signature(eset = "MethyLumiSet")`: ...

intensities.IB

  `signature(x = "MethyLumiSet", channel = "character")`: ...

intensities.IB

  `signature(x = "MethyLumiSet", channel = "missing")`: ...

intensities.M

  `signature(x = "MethyLumiSet", channel = "character")`: ...

intensities.M

  `signature(x = "MethyLumiSet", channel = "missing")`: ...

intensities.OOB.allelic

  `signature(x = "MethyLumiSet", channel = "character", allele = "character")`: ...

intensities.OOB.allelic

  `signature(x = "MethyLumiSet", channel = "missing", allele = "missing")`: ...

intensities.OOB

  `signature(x = "MethyLumiSet", channel = "character")`: ...

intensities.OOB

  `signature(x = "MethyLumiSet", channel = "missing")`: ...

intensities.U

  `signature(x = "MethyLumiSet", channel = "character")`: ...

intensities.U

  `signature(x = "MethyLumiSet", channel = "missing")`: ...

intensitiesByChannel

  `signature(object = "MethyLumiSet")`: ...

negctls.stderr

  `signature(object = "MethyLumiSet", channel = "character")`: ...

negctls.stderr

  `signature(object = "MethyLumiSet", channel = "missing")`: ...

negctls

  `signature(object = "MethyLumiSet", channel = "character")`: ...

negctls

  `signature(object = "MethyLumiSet", channel = "missing")`: ...

negnorm

  `signature(object = "MethyLumiSet", channel = "character")`: ...

negnorm

  `signature(object = "MethyLumiSet", channel = "missing")`: ...

normctls

  `signature(object = "MethyLumiSet")`: ...

plotSampleIntensities

  `signature(x = "MethyLumiSet")`: ...

probeNAs

  `signature(object = "MethyLumiSet")`: ...

sampleNAs

  `signature(object = "MethyLumiSet")`: ...

total.intensity

  `signature(object = "MethyLumiSet")`: ...

varFilter

  `signature(eset = "MethyLumiSet")`: ...

### Author(s)

Sean Davis & Tim Triche, Jr.

### See Also

`methylumiR`, `normalizeMethyLumiSet`, `methylumIDAT`, `MethyLumiQC`, `eSet`

### Examples

    showClass("MethyLumiSet")

[Package methylumi version 2.30.0 Index]