Class to Contain High-Throughput Assays and Experimental Metadata

Description

Container for high-throughput assays and experimental metadata. Classes derived from eSet contain one or more identical-sized matricies as assayData elements. Derived classes (e.g., ExpressionSet-class, SnpSet-class) specify which elements must be present in the assayData slot.

eSet object cannot be instantiated directly; see the examples for useage.

Creating Objects

eSet is a virtual class, so instances cannot be created.

Objects created under previous definitions of eSet-class can be coerced to classes derived based on eSet using updateOldESet.

Slots

Introduced in eSet:

assayData:

Contains matrices with equal dimensions, and with column number equal to nrow(phenoData). Class:AssayData-class

phenoData:

Contains variables describing sample (i.e., columns in assayData) phenotypes.Class: AnnotatedDataFrame-class

experimentData:

Contains details of experimental methods. Class: MIAME-class

annotation:

Label associated with the annotation package used in the experiment. Class:character

Methods

Methods defined in derived classes (e.g., ExpressionSet-class, SnpSet-class) may override the methods described here.

Class-specific methods:

sampleNames(object) and sampleNames(object)<-value:

Coordinate accessing and setting sample names in assayData and phenoData

featureNames(object), featureNames(object) <- value:

Coordinate accessing and setting of feature names (e.g, genes, probes) in assayData.

dims(object):

Access the common dimensions (dim) or column numbers (ncol), or dimensions of all memebers (dims) of assayData.

phenoData(object), phenoData(object) <- value:

Access and set phenoData.

varLabels(object), varLabels(eSet, value)<-:

Access and set variable labels in phenoData.

varMetadata(object), varMetadata(object) <- value:

Access and set descriptions of variables in phenoData.

pData(object), pData(object) <- value:

Access and set sample data information

varMetadata(object), varMetadata(eSet,value)

Access and set metadata describing variables reported in pData

experimentData(object),experimentData(object) <- value:

Access and set details of experimental methods

description(object),description(object) <- value:

Synonymous with experimentData; included for compatibility with exprSet.

notes(object),notes(object) <- value:

signature(object="eSet", value="list") Retrieve and set unstructured notes associated with eSet.

pubMedIds(object), pubMedIds(eSet,value)

Access and set PMIDs in experimentData.

abstract(object):

Access abstract in experimentData.

annotation(object), annotation(object) <- value

Access and set annotation label indicating package used in the experiment.

combine(eSet,eSet):

Combine two eSet objects. To be combined, eSets must have identical numbers of featureNames, distinct sampleNames, and identical annotation.

storageMode(object), storageMode(eSet,character)<-:

Change storage mode of assayData. Can be used to 'unlock' environments, or to change between list and environment modes of storing assayData.

reporterNames(object), reporterNames(object) <- value:

DEPRECATED, see featureNames

Standard generic methods:

initialize(object):

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 of features and samples; (2) the number and names of phenoData rows match the number and names of assayData columns

show(object)

Informatively display object contents.

dim(object), ncol

Access the common dimensions (dim) or column numbers (ncol), of all memebers (dims) of assayData.

object[(index):

Conducts subsetting of matrices and phenoData components

object, eSet$<-

Access and set named columns in phenoData

Additional functions:

updateOldESet

Update versions of eSet constructued using listOrEnv as assayData slot (before May, 2006)

Author(s)

Biocore team

See Also

Method use in ExpressionSet-class. Related classes AssayData-class, AnnotatedDataFrame-class, MIAME-class. Derived classes ExpressionSet-class, SnpSet-class. To update objects from previous class versions, see updateOldESet.

Examples

# create an instance of an existing derived class
new("ExpressionSet")

# update existing exprSet-like class to existing derived class
data(sample.exprSet)
expressionSet <- as(sample.exprSet,"ExpressionSet")
expressionSet

# update previous eSet-like class oldESet to existing derived class
## Not run: updateOldESet(oldESet, "ExpressionSet")

# create a new, ad hoc, class, for personal use
# all methods outlined above are available automatically
setClass("MySet", contains="eSet")
new("MySet")

# Create a more robust class, with initialization and validation methods
# to ensure assayData contains specific matricies
setClass("TwoColorSet", contains="eSet")

setMethod("initialize", "TwoColorSet",
          function(.Object,
                   phenoData = new("AnnotatedDataFrame"),
                   experimentData = new("MIAME"),
                   annotation = character(),
                   R = new("matrix"),
                   G = new("matrix"),
                   Rb = new("matrix"),
                   Gb = new("matrix"),
                   ... ) {
            callNextMethod(.Object,
                           phenoData = phenoData,
                           experimentData = experimentData,
                           annotation = annotation,
                           R=R, G=G, Rb=Rb, Gb=Gb,
                           ...)
          })

setValidity("TwoColorSet", function(object) {
  assayDataValidMembers(assayData(object), c("R", "G", "Rb", "Gb"))
})

new("TwoColorSet")

# eSet objects cannot be instantiated directly, only derived objects
try(new("eSet"))