Class "MethyLumiSet" for containing Illumina methylation data

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

Sean Davis & Tim Triche, Jr.

Examples

showClass("MethyLumiSet")
#> Class "MethyLumiSet" [package "methylumi"]
#> 
#> Slots:
#>                                                                
#> Name:                  QC            history          assayData
#> Class:       QCDataOrNULL         data.frame          AssayData
#>                                                                
#> Name:           phenoData        featureData     experimentData
#> Class: AnnotatedDataFrame AnnotatedDataFrame              MIAxE
#>                                                                
#> Name:          annotation       protocolData  .__classVersion__
#> Class:          character AnnotatedDataFrame           Versions
#> 
#> 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

Class `"MethyLumiSet"` for containing Illumina methylation data