MethyLumiQC-class {methylumi} | R Documentation

## Class `"MethyLumiQC"` for holding Illumina methylation QC data

### Description

This class inherits from the MethyLumi class (and therefore, from eSet in Biobase) and is designed to hold QC data from Illumina Beadstudio output. These data can be potentially useful when determining the cause for quality problems.

### Objects from the Class

Objects can be created by calls of the form `new("MethyLumiQC", assayData, phenoData, featureData, experimentData, annotation, betas)`.

### Slots

`assayData`:

  Object of class `"AssayData"`

`phenoData`:

  Object of class `"AnnotatedDataFrame"`

`featureData`:

  Object of class `"AnnotatedDataFrame"` containing the annotation columns from the Illumina Beadstudio output. In particular, the names of the probes describe the types of control probes.

`experimentData`:

  Object of class `"MIAME"`

`annotation`:

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

`.__classVersion__`:

  Object of class `"Versions"`

### Extends

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

### Methods

initialize

  `signature(.Object = "MethyLumiQC")`

Cy3.N

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

Cy3<-

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

Cy5.N

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

Cy5<-

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

QCdata<-

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

combine

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

controlData<-

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

controlTypes

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

hist

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

intensitiesByChannel

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

methylated

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

negctls.stderr

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

negctls.stderr

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

negctls

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

negctls

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

negnorm

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

negnorm

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

normctls

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

qcplot

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

unmethylated

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

### Author(s)

Sean Davis <sdavis2@mail.nih.gov>

### See Also

`methylumiR`, `MethyLumiSet`, `MethyLumi`, `eSet`

### Examples

    showClass("MethyLumiQC")

[Package methylumi version 2.26.0 Index]