NChannelSet-class(Biobase)
NChannelSet-class()所属R语言包：Biobase
Class to contain data from multiple channel array technologies
一类含有多通道阵列技术数据
译者：生物统计家园网 机器人LoveR
描述----------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".
高通量的检测和试验的元数据的容器。在一个单一的芯片包含多个（超过1）不同的“通道”的实验数据。在一个芯片上的所有通道都具有相同的一组offeatures“。实验由几个N沟道芯片的集合，每个芯片是一个“样本”。
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.
NChannelSet提供了一种配合型的信息和芯片注释数据的分析数据（表达式的值），它扩展了eSet类。
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
NChannelSet允许渠道提取（使用channels方法，下文提到），被选中的功能或样本的子集（使用[<features>, <samples>]）。选择和子集出现，使有关
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("NChannelSet", assayData, phenoData, ...). See the examples below.
创建对象可以通过检测的形式new("NChannelSet", assayData, phenoData, ...)。见下面的例子。
插槽----------Slots----------
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.
Object类的AssayData，通常是一个环境包含相同大小的矩阵。每个矩阵代表一个通道。每个矩阵中的列对应的样本，行功能。一旦创建，NChannelSet样品和渠道管理的协调。
Object of class AnnotatedDataFrame.
对象类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.
的dataAnnotatedDataFrame的组件是data.frame的样本数量等于行数。 data组件列对应测量的变项。
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.
包括强制性列varMetadata（labelDescription组件提供的每个列标签的文字描述）和datachannel组件。 channel varMetadata是：factor，assayData渠道的名称等于水平，加上特殊符号_ALL_。 channel列是用来表示信道（S）data组件AnnotatedDataFrame对应相应的列;_ALL_符号表示，data列是适用于所有通道。 varMetadata可能包含额外的列的任意信息。
Once created, NChannelSet coordinates selection and subsetting of channels in phenoData.
一旦创建，NChannelSet坐标phenoData选择的渠道和子集。
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.
Object类的AnnotatedDataFrame，用于包含的特征数据，这个实验是独一无二的;常见的功能级别描述一个特定的芯片通常是通过annotation插槽引用。
Object of class MIAME containing descriptions of the experiment.
类MIAME含实验描述的对象。
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
对象类"character"。一般长度字符串确定在实验过程中使用的芯片技术。注释字符串被用来检索信息
Object of class "character". A character vector identifying the dates the samples were scanned during the
对象类"character"。进行扫描，在一个确定的日期，样品的特征向量
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.
Object类的Versions，包含自动创建类定义BIOBASE包的版本，以及其他有关用户系统的信息在实例创建时的信息。使用的例子，请参阅classVersion和updateObject。
延伸----------Extends----------
Class "eSet", directly. Class "VersionedBiobase", by class "eSet", distance 2. Class "Versioned", by class "eSet", distance 3.
类"eSet"，直接。类"VersionedBiobase"，“ESET”级，距离为2。类"Versioned"，“ESET”级，距离3。
方法----------Methods----------
Methods with class-specific functionality:
类特定功能的方法：
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.
signature(object="NChannelSet", name="character")。返回ExperessionSet通道和相应的表型参数name创建。 name必须有长度为1。参数...很少使用，但传递给ExpressionSet构造，例如影响storage.mode。
signature(object = "NChannelSet"). Obtain names of channels contained in object.
signature(object = "NChannelSet")。获得所载object渠道名称。
signature(object = "NChannelSet", names = "character"). Create a new NChannelSet from object, containing only channels in names. The ... is not used by this method.
signature(object = "NChannelSet", names = "character")。创建一个新的NChannelSetobject，包含在names唯一渠道。“ ...不使用这种方法。
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.
signature(object = "NChannelSet", features = "ANY", samples = "ANY")。创建一个新的NChannelSet从object，包含匹配的唯一元素features和samples;任何索引可能丢失，或一个字符，数字或逻辑的向量。
signature(object = "NChannelSet", value = "list") assign each (named) element of value to the sampleNames of the correspondingly named elements of assayData in object.
signature(object = "NChannelSet", value = "list")value相应命名的元素sampleNamesassayDataobject分配给每个元素（命名）。
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.
eSet，annotation，annotation<-，assayData，assayData<-，classVersion，<X：classVersion<-派生功能的方法>，dim，dims，experimentData，experimentData<-，featureData，featureData<-，phenoData，phenoData<- protocolData，protocolData<-，pubMedIds，pubMedIds<-，sampleNames，sampleNames<-，storageMode，storageMode<-， varMetadata，varMetadata<-，isCurrent，isVersioned。
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)
其他方法：coerce（，对象之间的转换，如果可能的话），initialize（用于创建对象的内部），show（自动调用对象时显示在屏幕上）
作者（S）----------Author(s)----------
Martin Morgan <mtmorgan@fhcrc.org>
参见----------See Also----------
eSet, ExpressionSet.
eSet，ExpressionSet。
举例----------Examples----------
## An empty NChannelSet[＃空NChannelSet，]
obj <- new("NChannelSet")
## An NChannelSet with two channels (R, G) and no phenotypic data[＃NChannelSet两个通道（R，G），并没有表型数据]
obj <- new("NChannelSet",
R=matrix(0,10,5), G=matrix(0,10,5))
## An NChannelSet with two channels and channel-specific phenoData[＃NChannelSet两个通道和通道特定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 <- new("AnnotatedDataFrame",
data=data, varMetadata=varMetadata)
obj <- new("NChannelSet",
assayData=assayData, phenoData=phenoData)
obj
## G channel as NChannelSet[＃G通道作为NChannelSet]
selectChannels(obj, "G")
## G channel as ExpressionSet[＃G通道作为ExpressionSet]
channel(obj, "G")
## Samples "A" and "C"[＃样品的“A”和“C”]
obj[,c("A", "C")]
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 13:23:09
