MethyLumiQC-class: Class '"MethyLumiQC"' for holding Illumina methylation QC...
In seandavi/methylumi: Handle Illumina methylation data

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

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

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"

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

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"): ...