ExpressionSet(Biobase)
ExpressionSet()所属R语言包：Biobase
Class to Contain and Describe High-Throughput Expression Level Assays.
类来包含并说明高通量表达水平检测。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Container for high-throughput assays and experimental metadata. ExpressionSet class is derived from eSet, and requires a matrix named exprs as assayData member.
高通量的检测和试验的元数据的容器。 ExpressionSeteSet类派生，并要求名为exprs作为assayData成员的矩阵。
延伸----------Extends----------
Directly extends class eSet.
直接延伸类eSet。
创建对象----------Creating Objects----------
ExpressionSet instances are usually created through
ExpressionSet实例通常创建通过
ExpressionSet()
ExpressionSet()
ExpressionSet(assayData, phenoData=annotatedDataFrameFrom(assayData, byrow=FALSE), featureData=annotatedDataFrameFrom(assayData, byrow=TRUE), experimentData=new("MIAME"), annotation=character(), protocolData=annotatedDataFrameFrom(assayData, byrow=FALSE), ...) This creates an ExpressionSet with assayData provided explicitly. In this form, the only required named argument is assayData. assayData can be matrix (a matrix of expression data, with features corresponding to rows and samples to columns) or an environment that contains exprs.
ExpressionSet(assayData, phenoData=annotatedDataFrameFrom(assayData, byrow=FALSE), featureData=annotatedDataFrameFrom(assayData, byrow=TRUE), experimentData=new("MIAME"), annotation=character(), protocolData=annotatedDataFrameFrom(assayData, byrow=FALSE), ...) 这将创建一个ExpressionSet提供明确的assayData。在这种形式下，只需要命名参数是assayData。 assayData能matrix表达数据行和样品的列相应的功能（矩阵）或environment，包含exprs。
phenoData, featureData, experimentData, annotation, and protocolData can be missing, in which case they are assigned default values.
phenoData，featureData，experimentData，annotation，protocolData可以丢失，在这种情况下，他们被分配默认值。
插槽----------Slots----------
Inherited from eSet:
继承自eSet
assayData: Contains matrices with equal dimensions, and with column number equal to nrow(phenoData). assayData must contain a matrix exprs with rows represening features (e.g., reporters) and columns representing samples. Additional matrices of identical size (e.g., representing measurement errors) may
assayData：包含与同等尺寸的矩阵，列数等于nrow(phenoData)。 assayData必须包含一个矩阵与represening功能（如记者）和列代表样品行exprs。相同大小的附加矩阵（例如，代表测量误差）
phenoData: See eSet
phenoData：见eSet
featureData: See eSet
featureData：见eSet
experimentData: See eSet
experimentData：见eSet
annotation: See eSet
annotation：见eSet
protocolData: See eSet
protocolData：见eSet
方法----------Methods----------
Class-specific methods.
类的具体方法。
as(exprSet,"ExpressionSet") Coerce objects of
as(exprSet,"ExpressionSet")要挟对象
as(object,"data.frame") Coerce objects of ExpressionSet-class to data.frame by
as(object,"data.frame")ExpressionSet-classdata.frame由强制转换对象
exprs(ExpressionSet), exprs(ExpressionSet,matrix)<- Access and set elements named exprs in the AssayData-class
exprs(ExpressionSet)，exprs(ExpressionSet,matrix)<-访问集合中元素的名为exprsAssayData-class
...)</dt> 'apply'-like function to conveniently operate on
...）</代码> </ DT>“apply类似的功能，方便操作
write.exprs(ExpressionSet) Write expression values to a text file. It takes the same arguments as
write.exprs(ExpressionSet)表达式的值写入到一个文本文件。它以相同的参数
Derived from eSet:
来自eSet：
updateObject(object, ..., verbose=FALSE) Update instance to current version, if necessary. See updateObject and eSet
updateObject(object, ..., verbose=FALSE)实例更新到当前版本，如果有必要的。看到updateObject和eSet
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
assayData(ExpressionSet): See eSet
assayData(ExpressionSet)：见eSet
sampleNames(ExpressionSet) and sampleNames(ExpressionSet)<-: See eSet
sampleNames(ExpressionSet)和sampleNames(ExpressionSet)<-：见eSet
featureNames(ExpressionSet), featureNames(ExpressionSet, value)<-: See eSet
featureNames(ExpressionSet)，featureNames(ExpressionSet, value)<-：见eSet
dims(ExpressionSet): See eSet
dims(ExpressionSet)：见eSet
phenoData(ExpressionSet), phenoData(ExpressionSet,value)<-: See eSet
phenoData(ExpressionSet)，phenoData(ExpressionSet,value)<-：见eSet
varLabels(ExpressionSet), varLabels(ExpressionSet, value)<-: See eSet
varLabels(ExpressionSet)，varLabels(ExpressionSet, value)<-：见eSet
varMetadata(ExpressionSet), varMetadata(ExpressionSet,value)<-: See eSet
varMetadata(ExpressionSet)，varMetadata(ExpressionSet,value)<-：见eSet
pData(ExpressionSet), pData(ExpressionSet,value)<-: See eSet
pData(ExpressionSet)，pData(ExpressionSet,value)<-：见eSet
varMetadata(ExpressionSet), varMetadata(ExpressionSet,value) See eSet
varMetadata(ExpressionSet)，varMetadata(ExpressionSet,value)eSet
experimentData(ExpressionSet),experimentData(ExpressionSet,value)<-: See eSet
experimentData(ExpressionSet)，experimentData(ExpressionSet,value)<-：见eSet
pubMedIds(ExpressionSet), pubMedIds(ExpressionSet,value) See eSet
pubMedIds(ExpressionSet)，pubMedIds(ExpressionSet,value)eSet
abstract(ExpressionSet): See eSet
abstract(ExpressionSet)：见eSet
annotation(ExpressionSet), annotation(ExpressionSet,value)<- See eSet
annotation(ExpressionSet)，annotation(ExpressionSet,value)<-eSet
protocolData(ExpressionSet), protocolData(ExpressionSet,value)<- See eSet
protocolData(ExpressionSet)，protocolData(ExpressionSet,value)<-eSet
combine(ExpressionSet,ExpressionSet): See eSet
combine(ExpressionSet,ExpressionSet)：见eSet
storageMode(ExpressionSet), storageMode(ExpressionSet,character)<-: See eSet
storageMode(ExpressionSet)，storageMode(ExpressionSet,character)<-：见eSet
Standard generic methods:
标准的通用方法：
initialize(ExpressionSet): Object instantiation, used
initialize(ExpressionSet)：对象实例，使用
updateObject(ExpressionSet): Update outdated versions of ExpressionSet to their current definition. See
updateObject(ExpressionSet)：ExpressionSet他们目前的定义更新过时的版本。见
validObject(ExpressionSet): Validity-checking method, ensuring that exprs is a member of assayData. checkValidity(ExpressionSet) imposes this
validObject(ExpressionSet)：有效性检查方法，确保exprs是assayData的成员。 checkValidity(ExpressionSet)对本
Create a data package based on an ExpressionSet object. See
创建数据包基于一个ExpressionSet对象的。见
as(exprSet,ExpressionSet): Coerce exprSet to ExpressionSet.
as(exprSet,ExpressionSet)要挟exprSetExpressionSet。
as(eSet,ExpressionSet): Coerce the eSet portion of an object to ExpressionSet.
as(eSet,ExpressionSet)：强迫eSetExpressionSet对象部分。
show(ExpressionSet) See eSet
show(ExpressionSet)见eSet
dim(ExpressionSet), ncol See eSet
dim(ExpressionSet)，ncoleSet
ExpressionSet[(index): See eSet
ExpressionSet[(index)：见eSet
ExpressionSet$, ExpressionSet$<- See eSet
ExpressionSet$，ExpressionSet$<-eSet
ExpressionSet[[i]], ExpressionSet[[i]]<- See eSet
ExpressionSet[[i]]，ExpressionSet[[i]]<-eSet
作者（S）----------Author(s)----------
Biocore team
参见----------See Also----------
eSet-class, ExpressionSet-class.
eSet-class，ExpressionSet-class。
举例----------Examples----------
# create an instance of ExpressionSet[创建的ExpressionSet实例]
ExpressionSet()
ExpressionSet(assayData=matrix(runif(1000), nrow=100, ncol=10))
# update an existing ExpressionSet[更新现有的ExpressionSet]
data(sample.ExpressionSet)
updateObject(sample.ExpressionSet)
# information about assay and sample data[有关检测和样本数据信息]
featureNames(sample.ExpressionSet)[1:10]
sampleNames(sample.ExpressionSet)[1:5]
phenoData(sample.ExpressionSet)
experimentData(sample.ExpressionSet)
# subset: first 10 genes, samples 2, 4, and 10[子集：第10个基因，样品2，4，和10]
expressionSet <- sample.ExpressionSet[1:10,c(2,4,10)]
# named features and their expression levels[命名的功能及其表达水平]
subset <- expressionSet[c("AFFX-BioC-3_at","AFFX-BioDn-5_at"),]
exprs(subset)
# samples with above-average 'score' in phenoData[样品与高于平均水平的“得分”在phenoData]
highScores <- expressionSet$score > mean(expressionSet$score)
expressionSet[,highScores]
# (automatically) coerce to data.frame[（自动）要挟，以数据框]
lm(score~AFFX.BioDn.5_at + AFFX.BioC.3_at, data=subset)
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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。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
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发表于 2012-2-25 13:20:50
