eSet(Biobase)
eSet()所属R语言包：Biobase
Class to Contain High-Throughput Assays and Experimental Metadata
高通量的检测和试验的元数据类来包含
译者：生物统计家园网 机器人LoveR
描述----------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.
高通量的检测和试验的元数据的容器。派生类从eSet包含一个或多个assayData元素相同大小的矩阵。派生类（例如，ExpressionSet-class，SnpSet-class）指定哪些元素必须是在assayData插槽。
eSet object cannot be instantiated directly; see the examples for usage.
eSet对象不能被直接实例化;看到使用的例子。
创建对象----------Creating Objects----------
eSet is a virtual class, so instances cannot be created.
eSet是一个虚拟的类，所以不能创建实例。
Objects created under previous definitions of eSet-class can be coerced to the current classes derived from eSet using updateOldESet.
裹挟根据以前定义eSet-class的创建的对象，可以从eSet用updateOldESet的当前类。
插槽----------Slots----------
Introduced in eSet:
介绍eSet：
assayData: Contains matrices with equal dimensions, and with column number equal to
assayData：包含与同等尺寸的矩阵，列数等于
phenoData: Contains experimenter-supplied variables describing sample (i.e., columns in assayData) phenotypes.
phenoData：包含描述样本（即列在assayData）表型的实验者提供的变量。
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:
featureData：包含变量描述功能（即行中assayData）本实验所独有。使用annotation槽，有效地引用在实验中使用的注解包共同的特征数据。类别：
experimentData: Contains details of experimental
experimentData：包含实验的细节
annotation: Label associated with the annotation
annotation：标签与注释关联
protocolData: Contains microarray equipment-generated variables describing sample (i.e., columns in assayData) phenotypes.
protocolData：包含描述样本（即列在assayData）表型的芯片设备生成的变量。
.__classVersion__: A Versions object describing the R and Biobase version numbers used to created the instance.
.__classVersion__：VersionsR和BIOBASE版本用来创建实例的描述对象。
方法----------Methods----------
Methods defined in derived classes (e.g., ExpressionSet-class, SnpSet-class) may override the methods described here.
在派生类中定义的方法（例如，ExpressionSet-class，SnpSet-class）可能会覆盖这里所描述的方法。
Class-specific methods:
类的具体方法：
sampleNames(object)<-value:</dt> Coordinate accessing and setting
sampleNames(object)<-value：</ DT>坐标访问和设置
featureNames(object) <- value:</dt> Coordinate accessing and setting of
featureNames(object) <- value：</ DT>坐标访问和设置
dims(object): Access the common dimensions (dim) or column numbers (ncol), or dimensions of all members
dims(object)：进入（dim）或列号（ncol），或尺寸的所有成员共同的尺寸
phenoData(object) <- value:</dt> Access and set phenoData. Adding new columns to phenoData is often
phenoData(object) <- value：</ DT>访问并设置phenoData。添加新列phenoData往往是
pData(object), pData(object) <- value: Access and set sample data information. Adding new columns to pData is often
pData(object)，pData(object) <- value：访问和设置样本数据信息。添加新列pData往往是
varMetadata(eSet,value)</dt> Access and set metadata describing
varMetadata(eSet,value)</ DT>访问并设置元数据描述
value)<-:</dt> Access and set variable labels in
值）< - </代码>：</ DT>访问和设置变量标签
featureData(object) <- value:</dt> Access and set featureData.
featureData(object) <- value：</ DT>访问并设置featureData。
fData(object), fData(object) <- value: Access and set
fData(object)，fData(object) <- value：访问和设置
fvarMetadata(eSet,value)</dt> Access and set metadata describing
fvarMetadata(eSet,value)</ DT>访问并设置元数据描述
fvarLabels(eSet, value)<-:</dt> Access and set variable labels in
fvarLabels(eSet, value)<-：</ DT>访问和设置变量标签
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)
signature(object = "eSet", value = "AssayData")：访问和更换AssayData实例槽eSet。 assayData返回一个列表或环境;元素assayData不以其他方式访问（例如，通过exprs直接应用到eSet）
experimentData(object),experimentData(object) <- value: Access
experimentData(object)，experimentData(object) <- value：访问
description(object),description(object) <- value: Synonymous with experimentData.
description(object)，description(object) <- value：同义与experimentData。
signature(object="eSet", value="list") Retrieve and set unstructured notes associated with eSet. signature(object="eSet", value="character") As with
signature(object="eSet", value="list")检索和设置eSet相关的非结构化票据。 signature(object="eSet", value="character")与
pubMedIds(object), pubMedIds(eSet,value) Access
pubMedIds(object)，pubMedIds(eSet,value)访问
abstract(object): Access abstract in
abstract(object)：在访问抽象
annotation(object) <- value</dt> Access and set annotation label
annotation(object) <- value</ DT>访问和设置注释标签
protocolData(object) <- value</dt> Access and set the protocol data.
protocolData(object) <- value</ DT>访问和设置的协议数据。
preproc(object) <- value:</dt> signature(object="eSet", value="list") Access and set preprocessing information in the MIAME-class object associated with this
preproc(object) <- value：</ DT>signature(object="eSet", value="list")preprocessing与此相关的对象的访问和设置MIAME-class信息
combine(eSet,eSet): Combine two eSet objects. To be combined, eSets must have identical numbers of
combine(eSet,eSet)：合并两个eSet对象。要结合eSets必须有相同的数字
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
storageMode(object)，storageMode(eSet,character)<-：变化assayData存储模式。可用于“解锁”的环境，或改变list和environment模式之间
Standard generic methods:
标准的通用方法：
initialize(object): Object instantiation, can be called by
initialize(object)：对象实例，可以调用
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
validObject(object)：有效性检查方法，确保（1）所有assayData元件有相同的功能和样品数量;（2）数量和phenoData行的名称相匹配的数量和名称
as(eSet, "ExpressionSet") Convert instance of class "eSet" to instance of ExpressionSet-class, if possible.
as(eSet, "ExpressionSet")类的实例转换"eSet"实例ExpressionSet-class，如果可能的。
as(eSet, "MultiSet") Convert instance of class "eSet" to instance of MultiSet-class, if possible.
as(eSet, "MultiSet")类的实例转换"eSet"实例MultiSet-class，如果可能的。
updateObject(object, ..., verbose=FALSE) Update instance to current version, if necessary. Usually called through class inheritance rather than directly by the user. See updateObject
updateObject(object, ..., verbose=FALSE)实例更新到当前版本，如果有必要的。通常通过类的继承，而不是由用户直接调用。看到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
updateObjectTo(object, template, ..., verbose=FALSE)更新template插槽，如果有必要更新到当前版本的实例。通常所说的类继承，而不是直接用户。看到updateObjectTo
isCurrent(object) Determine whether version of object is current. See isCurrent
isCurrent(object)确定对象是否是最新的版本。看到isCurrent
isVersioned(object) Determine whether object contains a 'version' string describing its structure . See isVersioned
isVersioned(object)确定是否对象包含一个版本字符串，来描述它的结构。看到isVersioned
show(object) Informatively display object contents.
show(object)请提供知识显示对象内容。
dim(object), ncol Access the common dimensions (dim) or column numbers (ncol), of all
dim(object)，ncol进入（dim）或列号（ncol），所有常见的尺寸
object[(index): Conducts subsetting of matrices and
object[(index)：对矩阵进行子集和
object$name, object$name<-value Access and set name column in phenoData
object$name，object$name<-valuename访问和设置phenoData列
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
object[[i, ...]]，object[[i, ...]]<-value访问和设置列i（字符或数字索引）phenoData。 “......参数可以包含要添加的命名变量（特别是的labelDescription）
Additional functions:
附加功能：
assayDataElement(object, element) Return matrix
assayDataElement（对象，元素）返回矩阵
assayDataElement(object, element) <- value) Set element
assayDataElement（对象，元素）< - 值）集合元素
assayDataElementReplace(object, element, value) Set element
assayDataElementReplace（对象，元素值）集元素
assayDataElementNames(object) Return element names in
assayDataElementNames（对象）返回的元素名称
updateOldESet Update versions of eSet constructued using listOrEnv as assayData slot
updateOldESeteSetconstructued使用listOrEnvassayData槽更新版本
作者（S）----------Author(s)----------
Biocore team
参见----------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.
ExpressionSet-class方法使用。相关类AssayData-class，AnnotatedDataFrame-class，MIAME-class。派生类ExpressionSet-class，SnpSet-class。要更新从以前版本的类的对象，看到updateOldESet。
举例----------Examples----------
# update previous eSet-like class oldESet to existing derived class[以往ESET像类oldESet，更新现有的派生类]
## Not run: updateOldESet(oldESet, "ExpressionSet")[＃无法运行：updateOldESet（oldESet，“ExpressionSet”）]
# create a new, ad hoc, class, for personal use[创建一个新的，临时性的，个人使用的类，]
# all methods outlined above are available automatically[上述所有方法可用自动]
setClass("MySet", contains="eSet")
new("MySet")
# Create a more robust class, with initialization and validation methods[创建一个更强大的类，初始化和验证方法]
# to ensure assayData contains specific matricies[确保assayData包含特定的基质中]
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[ESET对象不能被直接实例化，只有派生的对象]
try(new("eSet"))
removeClass("MySet")
removeClass("TwoColorSet")
removeMethod("initialize", "TwoColorSet")
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
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发表于 2012-2-25 13:20:39
