FeatureSet-class {oligo} | R Documentation |
This is a class representation for oligonucleotide arrays at probe level. The main component are the intensities from multiple arrays of
the same design file. It is an extension of the eSet-class
.
Objects can be created by calls of the form new("FeatureSet", ...)
.
manufacturer
:"character"
describing the manufacturer.platform
:"character"
describing the design file associated to the object.assayData
:"listOrEnv"
as
described in eSet-class
.sampleNames
:"character"
with
the sample names.reporterNames
:"character"
with
the reporter names.description
:"MIAME"
notes
:"character"
with notes.annotation
:"character"
with annotation.history
:"character"
with history.reporterInfo
:"data.frameOrNULL"
phenoData
:"phenoData"
Class "eSet"
, directly.
Class "annotatedDataset"
, by class "eSet"
.
signature(object = "FeatureSet")
: extracts
allele information for SNP arrays.signature(x = "FeatureSet")
: produces boxplots.signature(object = "FeatureSet")
: Returns
the indexes of features on the array.signature(object = "FeatureSet")
: Returns
the names of the (PM) features.signature(object = "FeatureSet")
:
Returns the Platform Design Environment associated to the object.signature(x = "FeatureSet")
: Produces histograms.signature(x = "FeatureSet")
: Produces image plots.signature(object = "FeatureSet")
:
Returns the indexes in the PDEnv for given features.signature(x = "FeatureSet")
: Returns the number
of samples in the object.signature(object = "FeatureSet")
: Returns the
indexes for the MM features.signature(object = "FeatureSet")
: Assigns a value
to the MM matrix.signature(object = "FeatureSet")
: Returns the MM matrix.signature(x = "FeatureSet")
: Returns the number
of columns of the array.signature(object = "FeatureSet")
: Returns the
matrix with the number of pixels used.signature(x = "FeatureSet")
: Returns the number
of rows of the array.signature(object = "FeatureSet")
:
Returns the name of the PDEnv associated.signature(object = "FeatureSet")
: Returns the
type of the array.signature(object = "FeatureSet")
: Assigns a
type for the array.signature(object = "FeatureSet")
: Returns the
indexes for the PM features.signature(object = "FeatureSet")
: Assigns a value
to the PM matrix.signature(object = "FeatureSet")
: Returns the PM matrix.signature(object = "FeatureSet")
: Returns
the names of the features.signature(x = "FeatureSet")
: returns the matrix of
standard deviations.signature(object = "FeatureSet")
: Display basic
information about the array.signature(object = "FeatureSet")
: returns
the array manufacturer.signature(object = "FeatureSet")
: assigns
the array manufacturer.signature(object = "FeatureSet")
: returns
the matrix of intensities.
eSet-class