MethyLumiQC-class: Class '"MethyLumiQC"' for holding Illumina methylation QC...

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

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

1
showClass("MethyLumiQC")

seandavi/methylumi documentation built on Oct. 28, 2021, 12:42 a.m.