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 matrices 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 usage.

Creating Objects

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

Objects created under previous definitions of eSet-class can be coerced to the current classes derived from 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 experimenter-supplied variables describing sample (i.e., columns in assayData) phenotypes. Class: AnnotatedDataFrame-class

featureData:

Contains variables describing features (i.e., rows in assayData) unique to this experiment. Use the annotation slot to efficiently reference feature data common to the annotation package used in the experiment. 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

protocolData:

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

.__classVersion__:

A Versions object describing the R and Biobase version numbers used to created the instance. Intended for developer use.

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.

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

Also rownames and colnames; access and set feature and sample names.

dims(object):

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

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

Access and set phenoData. Adding new columns to phenoData is often more easily done with eSetObject[["columnName"]] <- value.

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

Access and set sample data information. Adding new columns to pData is often more easily done with eSetObject[["columnName"]] <- value.

varMetadata(object), varMetadata(eSet,value)

Access and set metadata describing variables reported in pData

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

Access and set variable labels in phenoData.

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

Access and set featureData.

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

Access and set feature data information.

fvarMetadata(object), fvarMetadata(eSet,value)

Access and set metadata describing features reported in fData

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

Access and set variable labels in featureData.

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

signature(object = "eSet", value = "AssayData"): Access and replace the AssayData slot of an eSet instance. assayData returns a list or environment; elements in assayData not accessible in other ways (e.g., via exprs applied directly to the eSet) can most reliably be accessed with, e.g., assayData(obj)[["se.exprs"]].

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

Access and set details of experimental methods

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

Synonymous with experimentData.

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

signature(object="eSet", value="list") Retrieve and set unstructured notes associated with eSet. signature(object="eSet", value="character") As with value="list", but append value to current list of notes.

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.

protocolData(object), protocolData(object) <- value

Access and set the protocol data.

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

signature(object="eSet", value="list") Access and set preprocessing information in the MIAME-class object associated with this eSet.

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.

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

as(eSet, "ExpressionSet")

Convert instance of class "eSet" to instance of ExpressionSet-class, if possible.

as(eSet, "MultiSet")

Convert instance of class "eSet" to instance of MultiSet-class, if possible.

updateObject(object, ..., verbose=FALSE)

Update instance to current version, if necessary. Usually called through class inheritance rather than directly by the user. See updateObject

updateObjectTo(object, template, ..., verbose=FALSE)

Update instance to current version by updating slots in template, if necessary. Usually call by class inheritance, rather than directly by the user. See updateObjectTo

isCurrent(object)

Determine whether version of object is current. See isCurrent

isVersioned(object)

Determine whether object contains a 'version' string describing its structure . See isVersioned

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$name, object$name<-value

Access and set name column in phenoData

object[[i, ...]], object[[i, ...]]<-value

Access and set column i (character or numeric index) in phenoData. The ... argument can include named variables (especially labelDescription) to be added to varMetadata.

Additional functions:

assayDataElement(object, element)

Return matrix element from assayData slot of object.

assayDataElement(object, element, validate=TRUE) <- value)

Set element element in assayData slot of object to matrix value. If validate=TRUE, check that value row and column names of conform to object.

assayDataElementReplace(object, element, value, validate=TRUE)

Set element element in assayData slot of object to matrix value. If validate=TRUE, check that row and column names of value conform to object.

assayDataElementNames(object)

Return element names in assayData slot of object

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

# 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
.MySet <- setClass("MySet", contains="eSet")
.MySet()

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

TwoColorSet <-
    function(phenoData=AnnotatedDataFrame(), experimentData=MIAME(),
             annotation=character(), R=new("matrix"), G=new("matrix"),
             Rb=new("matrix"), Gb=new("matrix"), ...)
{
    .TwoColorSet(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"))
})

TwoColorSet()

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

removeClass("MySet")
removeClass("TwoColorSet")