R语言 MSnbase包 MSnSet-class()函数中文帮助文档(中英文对照)

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MSnSet-class(MSnbase)
MSnSet-class()所属R语言包：MSnbase

                                         The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
                                         类为MS蛋白质组表达数据和元数据的的“MSnSet”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

The MSnSet holds quantified expression data for MS proteomics data and the experimental meta-data. The MSnSet class is derived from the "eSet" class and mimics the "ExpressionSet" class classically used for microarray data.
MSnSet保存为MS蛋白质组学数据的量化表达数据和实验的元数据。来自MSnSet类"eSet"类模仿"ExpressionSet"类经典芯片的数据。


类的对象----------Objects from the Class----------

Objects can be created by calls of the form new("MSnSet", exprs, ...). See also "ExpressionSet" for helpful information. Expression data produced from other softwares can thus make use of this standardized data container to benefit R and Bioconductor packages. Importer functions will be developed to stream-line the generation of "MSnSet" instances from third-party software.
创建对象可以通过检测的形式new("MSnSet", exprs, ...)。也看到"ExpressionSet"有用的信息。从其他软件产生的基因表达数据，从而使这个标准化的数据容器的利用，以造福R和Bioconductor包。进口商将开发功能流线"MSnSet"来自第三方软件的情况下产生的。

In the frame of the MSnbase package, MSnSet instances are generated from "MSnExp" experiments when the "ReporterIons" using the "quantify" method).
框在MSnbase包，MSnSet的"MSnExp"实验生成实例时"ReporterIons"使用"quantify"方法）。


插槽----------Slots----------




qual: Object of class "data.frame" that records peaks data for each of the reporter ions to be used as quality
qual：Object类的"data.frame"记录峰每个记者离子的数据将作为质量




processingData: Object of class
processingData：对象类




assayData: Object of class "assayData" containing a matrix with equal with column number equal to nrow(phenoData). assayData must contain a matrix exprs with rows represening features (e.g., reporters ions) and columns representing samples. See the "AssayData" class, exprs and assayData accessor for more details. This slot in indirectly inherited from
assayData：Object类的"assayData"含等于矩阵的列数等于nrow(phenoData)。 assayData必须包含一个矩阵与represening功能（例如，记者离子）和列，占样本行exprs。见"AssayData"类exprs和assayData存取更多细节。这槽间接继承




phenoData: Object of class "AnnotatedDataFrame" containing experimenter-supplied variables describing sample (i.e the individual tags for an labelled MS experiment) (indireclty  inherited from  "eSet"). See phenoData and the "eSet"
phenoData：Object类的"AnnotatedDataFrame"含实验者提供的变量描述样本（即单个标签标记MS实验）（indireclty继承"eSet"）。看到phenoData和"eSet"




featureData: Object of class "AnnotatedDataFrame" containing variables describing features (spectra in our case), e.g. identificaiton data, peptide sequence, identification score,... (inherited indirectly from  "eSet"). See featureData and the "eSet"
featureData：类"AnnotatedDataFrame"包含变量描述功能对象（在本例中的光谱），例如： identificaiton数据，肽序列，鉴定得分，... （从"eSet"间接继承）。看到featureData和"eSet"




experimentData: Object of class "MIAPE", containing details of experimental methods (inherited from "eSet"). See  experimentData and the "eSet"
experimentData：Object类的"MIAPE"，包含实验方法的细节（"eSet"继承）。看到experimentData和"eSet"




annotation:  not used here.
annotation：这里不使用。




protocolData: Object of class "AnnotatedDataFrame" containing equipment-generated variables (inherited indirectly from "eSet"). See protocolData and the "eSet"
protocolData类"AnnotatedDataFrame"包含设备生成的变量（从"eSet"间接继承）的对象。看到protocolData和"eSet"




.__classVersion__: Object of class "Versions" describing the versions of R, the Biobase package, "eSet", "pSet" and MSnSet of the current instance. Intended for developer use and debugging (inherited
.__classVersion__：Object类的"Versions"描述的R，BIOBASE包的版本，"eSet"，"pSet"和MSnSet当前实例。供开发人员使用和调试（继承


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----------

MSnSet specific methods or over-ridding it's super-class are described below. See also more "eSet" for inherited methods.
下面介绍MSnSet的具体方法，摆脱它的超类。见也更"eSet"继承的方法。




dim signature(x = "MSnSet"): Returns the dimensions of object's assay data, i.e the number of samples and the number of
暗淡signature(x = "MSnSet")：返回对象的检测数据的尺寸，即样品的数量和数量




fileNames signature(object = "MSnSet"): Access file
文件名signature(object = "MSnSet")：Access文件




msInfo signature(object = "MSnSet"): Prints the MIAPE-MS
MSINFOsignature(object = "MSnSet")：打印的MIAPE的质谱




processingData signature(object = "MSnSet"): Access the
processingDatasignature(object = "MSnSet")：进入




show signature(object = "MSnSet"): Displays object
显示signature(object = "MSnSet")：显示对象




qual signature(object = "MSnSet"): Access the reporter
QUALsignature(object = "MSnSet")：访问记者




purityCorrect signature(object = "MSnSet", impurities =         "matrix"): performs reporter ions purity correction. See
purityCorrectsignature(object = "MSnSet", impurities =         "matrix")：执行记者离子纯度校正。见




meanSdPlot signature(object = "MSnSet"): Plots row standard deviations versus row means. See
meanSdPlotsignature(object = "MSnSet")：图解行与行方式的标准偏差。见




normalise signature(object = "MSnSet"): Performs MSnSet normalisation. See normalise for more
标准化signature(object = "MSnSet")：执行MSnSet标准化。 normalise




t signature(x = "MSnSet"): Returns a transposed MSnSet object where features are now aligned along columns  and samples along rows and the phenoData and featureData slots have been swapped. The
Tsignature(x = "MSnSet")：返回转置MSnSet功能现在沿行列，并沿样品一致phenoData和featureData槽已交换的对象。 “




as(,"ExpressionSet") signature( x = "MSnSet"): Coerce object from MSnSet to ExpressionSet-class. The experimentData slot is
（“ExpressionSet”）signature( x = "MSnSet")从MSnSetExpressionSet-class：强制转换对象。 experimentData插槽




write.exprs signature(x = "MSnSet")
write.exprs签名（=“MSnSet”）

Writes expression values to a tab-separated file (default is tmp.txt). The fDataCols parameter can be used to specify which featureData columns (as column names, column number or logical) to append on the right of the expression matrix.  The following arguments are the same as write.table.
表达式的值写入到一个制表符分隔的文件（默认是tmp.txt）。 fDataCols参数可以用来指定featureData列（如列名，列数或logical）追加表达矩阵权。以下参数是相同的write.table。


作者（S）----------Author(s)----------



Laurent Gatto <lg390@cam.ac.uk>




参见----------See Also----------

"eSet" and "ExpressionSet". MSnSet quantitation values can be exported to a file with write.exprs.
"eSet"和"ExpressionSet"。 MSnSet定量值可以导出一个write.exprs文件。


举例----------Examples----------


mzxmlfile <- dir(system.file("extdata",package="MSnbase"),
                 pattern="mzXML",full.names=TRUE)
msnexp <- readMSData(mzxmlfile,verbose=FALSE)
msnset <- quantify(msnexp,method="trap",reporters=iTRAQ4,verbose=FALSE)
msnset

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