ReporterIons-class(MSnbase)
ReporterIons-class()所属R语言包：MSnbase
The "ReporterIons" Class
“ReporterIons”级
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The ReporterIons class allows to define a set of isobaric reporter ions that are used for quantification in MSMS mode, e.g. iTRAQ (isobaric tag for relative and absolute quantitation) or TMT (tandem mass tags). ReporterIons instances can them be used when quantifying "MSnExp" data of plotting the reporters peaks based on in "Spectrum2" ojects.
ReporterIons类，允许定义了一套恒压记者离子量化使用在MSMS模式，例如iTRAQ的（相对和绝对定量的等标签）或TMT（串联质谱标签）。 ReporterIons实例，它们可以被量化"MSnExp"数据绘制记者在"Spectrum2" ojects基于峰时使用。
Some reporter ions are provided with MSnbase an can be loaded with the data function. These reporter ions data sets are:
一些记者离子MSnbase具有data功能可以加载。这些记者离子数据集是：
iTRAQ4: ReporterIon object for the iTRAQ
iTRAQ4：ReporterIon的iTRAQ的对象
iTRAQ5: ReporterIon object for the iTRAQ
iTRAQ5：ReporterIon的iTRAQ的对象
TMT6: ReporterIon object for the TMT
TMT6：ReporterIon对象为TMT
TMT7: ReporterIon object for the TMT
TMT7：ReporterIon对象为TMT
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("ReporterIons", ...).
创建对象可以通过检测的形式new("ReporterIons", ...)。
插槽----------Slots----------
name: Object of class "character" to identify
name：Object类的"character"查明
reporterNames: Object of class "character" naming each individual reporter of the ReporterIons instance. If not provided explicitely, they are names by concatenating the ReporterIons name and the respective MZ
reporterNames：Object类的"character"命名每个个别记者ReporterIons实例。如果没有明确地规定，他们的名字串连ReporterIons的名称和相应的锰锌
description: Object of class "character" to
类的对象description："character"
mz: Object of class "numeric" providing the MZ
mz：Object类的"numeric"提供的MZ
col: Object of class "character" providing
col：Object类的"character"提供
width: Object of class "numeric" indicating the width around the individual reporter ions MZ values were to search for peaks. This is dependent on the mass spectrometer's resolution and is used for peak picking when quantifying the reporters. See
width：Object类的"numeric"周围的个别记者离子锰锌值的宽度为峰搜索。这是依赖于质谱仪的分辨率和量化的记者时，高峰采摘。见
.__classVersion__: Object of class "Versions" indicating the version of the ReporterIons
.__classVersion__：Object类的"Versions"说明ReporterIons版本
延伸----------Extends----------
Class "Versioned", directly.
类"Versioned"，直接。
方法----------Methods----------
show(object) Displays object content as text.
show(object)对象显示为文本的内容。
object[] Subsets one or several reporter ions of the ReporterIons object and returns a new instance of the same
object[]或ReporterIons对象的一个子集，几个记者离子和返回一个相同的新的实例
length(object) Returns the number of reporter ions in
length(object)返回的记者离子数量
mz(object) Returns the expected mz values of reporter
mz(object)返回预期的记者MZ值
Returns the colours used to highlight the reporter ions.
返回用来突出记者离子的颜色。
reporterNames(object) Returns the name of the individual reporter ions. If not specified or is an incorrect number of names is provided at initialisation, the names are generated automatically by concatenating the instance name and the
reporterNames(object)返回个别记者离子的名称。如果没有指定或不正确的名称是在初始化提供的名称自动生成，通过连接实例名称和
reporterNames(object) <- value Sets the reporter names to value, which must be a character of the same
reporterNames(object) <- value设置为value记者名称，它必须是相同的字符
width(object) Returns the widths in which the
width(object)返回的宽度在其中
names(object) Returns the name of the
names(object)返回的名称
description(object) Returns the description of the
description(object)返回的描述
作者（S）----------Author(s)----------
Laurent Gatto <lg390@cam.ac.uk>
参考文献----------References----------
Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ. "Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents." Mol Cell Proteomics, 2004 Dec;3(12):1154-69. Epub 2004 Sep 22. PubMed PMID: 15385600.
Neumann T, Johnstone R, Mohammed AK, Hamon C. "Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS." Anal Chem. 2003 Apr 15;75(8):1895-904. Erratum in: Anal Chem. 2006 Jun 15;78(12):4235. Mohammed, A Karim A [added] and Anal Chem. 2003 Sep 15;75(18):4942. Johnstone, R [added]. PubMed PMID: 12713048.
参见----------See Also----------
TMT6 or iTRAQ4 for readily available examples.
TMT6或iTRAQ4现成的例子。
举例----------Examples----------
## Code used for the iTRAQ4 set[＃代码用于iTRAQ4集]
ri <- new("ReporterIons",
description="4-plex iTRAQ",
name="iTRAQ4",
reporterNames=c("iTRAQ4.114","iTRAQ4.115",
"iTRAQ4.116","iTRAQ4.117"),
mz=c(114.1,115.1,116.1,117.1),
col=c("red","green","blue","yellow"),
width=0.05)
ri
reporterNames(ri)
ri[1:2]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
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发表于 2012-2-26 07:32:24
