FeatureSet-class {oligo}R Documentation

Class "FeatureSet"

Description

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 from the Class

Objects can be created by calls of the form new("FeatureSet", ...).

Slots

manufacturer:
Object of class "character" describing the manufacturer.
platform:
Object of class "character" describing the design file associated to the object.
assayData:
Object of class "listOrEnv" as described in eSet-class.
sampleNames:
Object of class "character" with the sample names.
reporterNames:
Object of class "character" with the reporter names.
description:
Object of class "MIAME"
notes:
Object of class "character" with notes.
annotation:
Object of class "character" with annotation.
history:
Object of class "character" with history.
reporterInfo:
Object of class "data.frameOrNULL"
phenoData:
Object of class "phenoData"

Extends

Class "eSet", directly. Class "annotatedDataset", by class "eSet".

Methods

allele
signature(object = "FeatureSet"): extracts allele information for SNP arrays.
boxplot
signature(x = "FeatureSet"): produces boxplots.
featureIndex
signature(object = "FeatureSet"): Returns the indexes of features on the array.
geneNames
signature(object = "FeatureSet"): Returns the names of the (PM) features.
getPlatformDesign
signature(object = "FeatureSet"): Returns the Platform Design Environment associated to the object.
hist
signature(x = "FeatureSet"): Produces histograms.
image
signature(x = "FeatureSet"): Produces image plots.
indexFeatureSetName
signature(object = "FeatureSet"): Returns the indexes in the PDEnv for given features.
length
signature(x = "FeatureSet"): Returns the number of samples in the object.
mmindex
signature(object = "FeatureSet"): Returns the indexes for the MM features.
mm<-
signature(object = "FeatureSet"): Assigns a value to the MM matrix.
mm
signature(object = "FeatureSet"): Returns the MM matrix.
ncol
signature(x = "FeatureSet"): Returns the number of columns of the array.
npixels
signature(object = "FeatureSet"): Returns the matrix with the number of pixels used.
nrow
signature(x = "FeatureSet"): Returns the number of rows of the array.
platformDesignName
signature(object = "FeatureSet"): Returns the name of the PDEnv associated.
platform
signature(object = "FeatureSet"): Returns the type of the array.
platform<-
signature(object = "FeatureSet"): Assigns a type for the array.
pmindex
signature(object = "FeatureSet"): Returns the indexes for the PM features.
pm<-
signature(object = "FeatureSet"): Assigns a value to the PM matrix.
pm
signature(object = "FeatureSet"): Returns the PM matrix.
probeNames
signature(object = "FeatureSet"): Returns the names of the features.
sd
signature(x = "FeatureSet"): returns the matrix of standard deviations.
show
signature(object = "FeatureSet"): Display basic information about the array.
manufacturer
signature(object = "FeatureSet"): returns the array manufacturer.
manufacturer<-
signature(object = "FeatureSet"): assigns the array manufacturer.
exprs
signature(object = "FeatureSet"): returns the matrix of intensities.

See Also

eSet-class


[Package oligo version 0.99.15 Index]