Class to contain data from multiple channel array technologies

Description

Container for high-throughput assays and experimental meta-data. Data are from experiments where a single ‘chip’ contains several (more than 1) different ‘channels’. All channels on a chip have the same set of‘features’. An experiment consists of a collection of several N-channel chips; each chip is a ‘sample’.

An NChannelSet provides a way to coordinate assay data (expression values) with phenotype information and references to chip annotation data; it extends the eSet class.

An NChannelSet allows channels to be extracted (using the channels method, mentioned below), and subsets of features or samples to be selected (using [<features>, <samples>]). Selection and subsetting occur so that relevant phenotypic data is maintained by the selection or subset.

Objects from the Class

Objects can be created by calls of the form NChannelSet( assayData, phenoData, ...). See the examples below.

Slots

assayData:

Object of class AssayData, usually an environment containing matrices of identical size. Each matrix represents a single channel. Columns in each matrix correspond to samples, rows to features. Once created, NChannelSet manages coordination of samples and channels.

phenoData:

Object of class AnnotatedDataFrame.

The data component of the AnnotatedDataFrame is data.frame with number of rows equal to the number of samples. Columns of the data component correspond to measured covariates.

The varMetadata component consists of mandatory columns labelDescription (providing a textual description of each column label in the data component) and channel. The channel of varMetadata is a factor, with levels equal to the names of the assayData channels, plus the special symbol _ALL_. The channel column is used to indicate which channel(s) the corresponding column in the data component of AnnotatedDataFrame correspond; the _ALL_ symbol indicates that the data column is applicable to all channels. varMetadata may contain additional columns with arbitrary information.

Once created, NChannelSet coordinates selection and subsetting of channels in phenoData.

featureData:

Object of class AnnotatedDataFrame, used to contain feature data that is unique to this experiment; feature-level descriptions common to a particular chip are usually referenced through the annotation slot.

experimentData:

Object of class MIAME containing descriptions of the experiment.

annotation:

Object of class "character". Usually a length-1 character string identifying the chip technology used during the experiment. The annotation string is used to retrieve information about features, e.g., using the annotation package.

protocolData:

Object of class "character". A character vector identifying the dates the samples were scanned during the experiment.

.__classVersion__:

Object of class Versions, containing automatically created information about the class definition Biobase package version, and other information about the user system at the time the instance was created. See classVersion and updateObject for examples of use.

Extends

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

Methods

Methods with class-specific functionality:

channel(object, name, ...)

signature(object="NChannelSet", name="character"). Return an ExperessionSet created from the channel and corresponding phenotype of argument name. name must have length 1. Arguments ... are rarely used, but are passed to the ExpressionSet constructor, for instance to influence storage.mode.

channelNames(object), channelNames(object) <- value

signature(object = "NChannelSet"). Obtain, reorder, or rename channels contained in object. See channelNames.

selectChannels(object, names, ...

signature(object = "NChannelSet", names = "character"). Create a new NChannelSet from object, containing only channels in names. The ... is not used by this method.

object[features, samples]

signature(object = "NChannelSet", features = "ANY", samples = "ANY"). Create a new NChannelSet from object, containing only elements matching features and samples; either index may be missing, or a character, numeric, or logical vector.

sampleNames(object) <- value

signature(object = "NChannelSet", value = "list") assign each (named) element of value to the sampleNames of the correspondingly named elements of assayData in object.

Methods with functionality derived from eSet: annotation, annotation<-, assayData, assayData<-, classVersion, classVersion<-, dim, dims, experimentData, experimentData<-, featureData, featureData<-, phenoData, phenoData<-, protocolData, protocolData<-, pubMedIds, pubMedIds<-, sampleNames, sampleNames<-, storageMode, storageMode<-, varMetadata, varMetadata<-, isCurrent, isVersioned, updateObject.

Additional methods: coerce (‘as’, to convert between objects, if possible), initialize (used internally for creating objects), show (invoked automatically when the object is displayed to the screen)

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

See Also

eSet, ExpressionSet.

Examples

## An empty NChannelSet
obj <- NChannelSet()

## An NChannelSet with two channels (R, G) and no phenotypic data
obj <- NChannelSet(R=matrix(0,10,5), G=matrix(0,10,5))

## An NChannelSet with two channels and channel-specific phenoData
R <- matrix(0, 10, 3, dimnames=list(NULL, LETTERS[1:3]))
G <- matrix(1, 10, 3, dimnames=list(NULL, LETTERS[1:3]))
assayData <- assayDataNew(R=R, G=G)
data <- data.frame(ChannelRData=numeric(ncol(R)),
                   ChannelGData=numeric(ncol(R)),
                   ChannelRAndG=numeric(ncol(R)))
varMetadata <- data.frame(labelDescription=c(
                            "R-specific phenoData",
                            "G-specific phenoData",
                            "Both channel phenoData"),
                          channel=factor(c("R", "G", "_ALL_")))
phenoData <- AnnotatedDataFrame(data=data, varMetadata=varMetadata)
obj <- NChannelSet(assayData=assayData, phenoData=phenoData)
obj

## G channel as NChannelSet
selectChannels(obj, "G")

## G channel as ExpressionSet
channel(obj, "G")

## Samples "A" and "C"
obj[,c("A", "C")]