Description Objects from the Class Slots Extends Methods Author(s) See Also Examples
Container for high-throughput assays and experimental
metadata. "BeadSetIllumina"
class is derived from
"eSet"
and requires matrices
“R”, “G”, “se.R”, “se.G”, and “no.beads” as
assay data members
new("BeadSetIllumina", ...)
new("BeadSetIllumina",
phenoData = [AnnotatedDataFrame],
featureData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
R = [matrix],
G = [matrix],
se.R = [matrix],
se.G = [matrix],
no.beads = [matrix],
...)
"BeadSetIllumina"
instances are usually created from bead type
summary text-files using readBeadSummaryOutput
assayData
:Object of class "AssayData"
,
with storage mode “list”. Contains data-matrices with
rows corresponding to markers and columns to samples/arrays. Required
members are “R”, “G”, “se.R”, “se.G”, and
“no.beads”.
phenoData
:Object of class "AnnotatedDataFrame"
with additional information about the samples.
featureData
:Object of class
"AnnotatedDataFrame"
with additional information about the
markers.
experimentData
:Object of class "MIAME"
annotation
:Object of class "character"
.__classVersion__
:Object of class "Versions"
Class "eSet"
, directly.
Class "VersionedBiobase"
, by class "eSet", distance 2.
Class "Versioned"
, by class "eSet", distance 3.
Class-specific methods:
initialize
signature(.Object = "BeadSetIllumina")
:
Object instantiation, can be called by derived classes but not usually by the user.
validObject(object)
:Validity-checking method,
ensuring (1) all assayData
components have the same number and names of
features and samples; (2) the number and names of phenoData
and featureData
rows match the number and names of
assayData
columns and rows, respectively; (3)
storageMode(object)
is set to “list”
A selection of methods inherited from "eSet"
:
sampleNames(object)
,
sampleNames(object) <- value
:See "eSet"
featureNames(object)
,
featureNames(object) <- value
:See "eSet"
phenoData(object)
,
phenoData(object) <- value
:See "eSet"
pData(object)
, pData(object) <- value
:See "eSet"
varMetadata(object)
See "eSet"
varLabels(object)
See "eSet"
featureData(object)
,
featureData(object) <- value
:See "eSet"
fData(object)
, fData(object) <- value
:See "eSet"
fvarMetadata(object)
See "eSet"
fvarLabels(object)
See "eSet"
assayData(object), assayData(object) <- value
:See "eSet"
combine(object,object1)
:See "eSet"
storageMode(object)
:See
"eSet"
. Do not assign new values to
storageMode
, as this could render the object invalid
Lars Gidskehaug
readBeadSummaryOutput
, preprocessBeadSet
,
createAlleleSet
, AlleleSetIllumina
,
eSet
1 | showClass("BeadSetIllumina")
|
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