IBSpectra-class(isobar)
IBSpectra-class()所属R语言包：isobar
IBSpectra Class for Isobarically Tagged Quantitative MS
IBSpectra类为恒压标记的定量质谱
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class represents a quantitative MS proteomics experiment labeled using Isobaric tags (iTRAQ, TMT). IBSpectra is a abstract class which is implemented in the IBSpectraTypes classes iTRAQ4plexSpectra, iTRAQ8plexSpectra, TMT2plexSpectra and TMT6plexSpectra.
这个类表示一个定量的MS蛋白质组学实验使用等压标记（iTRAQ的，TMT）的标记。 “IBSpectra是一个抽象类，在实施IBSpectraTypes类iTRAQ4plexSpectra，iTRAQ8plexSpectra，TMT2plexSpectra和TMT6plexSpectra。
It contains per-spectrum meassurements of the reporter tag intensity and m/z in assayData, and protein grouping in proteinGroup.
它包含了每频谱meassurements记者标记强度和m / z在assayData，蛋白质在proteinGroup分组。
类的对象----------Objects from the Class----------
IBSpectra objects are typically created using the readIBSpectra method or by calls of the form new("iTRAQ4plexSpectra",data=NULL,data.ions=NULL,...).
IBSpectra对象通常使用readIBSpectra方法创建或检测的形式new("iTRAQ4plexSpectra",data=NULL,data.ions=NULL,...).
插槽----------Slots----------
IBSpectra extends eSet which is a container for high-throughput assays and experimental metadata. Slots introduced in eSet (for more details on slots and methods refer to eSet help):
IBSpectra延伸eSet这是一种高通量的检测和试验的元数据的容器。 eSet帮助）eSet介绍插槽（更多细节插槽和方法是指：
assayData: Contains matrices 'ions' and 'mass storing reporter tag intensities and m/z values for each tag and spectrum. Can be accessed by reporterIntensities
assayData：包含矩阵“离子”和“大规模储存记者标记强度和m / z值，为每一个标签和频谱。可以访问reporterIntensities
phenoData: Contains experimenter-supplied variables describing phenotypes behind reporter tags.
phenoData：包含实验者提供的变量描述记者标签背后的表型。
featureData: Describes the spectra's retention time, charge, peptide sequence, etc and can be accessed by
featureData：描述光谱的停留时间，费用，肽序列等，并可以访问
experimentData: Contains details of experimental
experimentData：包含实验的细节
annotation: UNUSED. Label associated with the annotation
annotation：未使用。与注释相关的标签
protocolData: UNUSED. Contains equipment-generated
protocolData：未使用。包含设备产生
log: character matrix logging isotope impurity
log：character matrix测井同位素杂质
Slots introduced in IBSpectra:
插槽IBSpectra介绍：
proteinGroup: A ProteinGroup object describing peptide and protein identifications
proteinGroup：一个ProteinGroup对象描述肽和蛋白质的鉴定
reporterTagNames: A character vector denoting the
reporterTagNames：一个特征向量表示
reporterMasses: The 'true' m/z of the reporter tags in the MS/MS spectrum, used to isolate m/z-intensity pairs from
reporterMasses的真正的M / Z的MS / MS谱中的记者标签，用于隔离的m / z强度对
isotopeImpurities: Manufacturer supplied isotope impurities, need to be set per batch and used for correction by correctIsotopeImpurities.
isotopeImpurities：制造商提供的同位素杂质，每批需要设置，使用和校正correctIsotopeImpurities。
构造----------Constructor----------
See readIBSpectra for creation based on peaklist (e.g. MGF format) and identification files (Mascot and Phenyx output).
看到readIBSpectra创造的基础上peaklist（如MGF的格式）和鉴定文件（吉祥物和Phenyx输出）。
Creates a IBSpectra object.
创建一个IBSpectra对象。
type Denotes the type of IBSpectra, either 'iTRAQ4plexSpectra','iTRAQ8plexSpectra','TMT2plexSpectra' or 'TMT6plexSpectra'. Call IBSpectraTypes() to see a list of the implemented types.
type表示的IBSpectra类型，要么“iTRAQ4plexSpectra，iTRAQ8plexSpectra，TMT2plexSpectra或TMT6plexSpectra。致电IBSpectraTypes（）实施类型的列表。
data A 'data.frame' in a ibspectra-csv format.
dataA“数据框”在ibspectra csv格式。
强迫----------Coercion----------
In the code snippets below, x is a IBSpectra object. IBSpectra object can be coerced to
在下面的代码片段，x是IBSpectra对象。 IBSpectra对象可以强制转换为
as(x, "data.frame"): Creates a data.frame containing all identification and quantitation information. Peptide matching
as(x, "data.frame")：创建一个数据框包含所有识别和定量信息。肽匹配
as(x, "data.frame.concise"): Creates a data.frame containing all identification and quantitation information. Proteins are concatenated - so the
as(x, "data.frame.concise")：创建一个数据框包含所有识别和定量信息。蛋白质串联 - 所以
Coerces to a MSnSet object (package
胁迫MSnSet对象（包
Coerces a MSnSet to IBSpectra object.
胁迫一MSnSetIBSpectra对象。
存取----------Accessors----------
In the following code snippets, x is a IBSpectra object.
在下面的代码片段，x是IBSpectra对象。
proteinGroup(x): Gets and sets the ProteinGroup.
proteinGroup(x)：获取并设置ProteinGroup。
isotopeImpurities(x): Gets and sets the isotope impurities of the isobaric tags as defined by the manufacturers
isotopeImpurities(x)：获取和设置等压标记的同位素杂质由厂家定义
Gets and sets the element ('ions' or 'mass') for each tag and spectrum. '...' is handed down to spectrumSel, so it is possible to select for peptides or proteins.
获取和设置元素（“离子”或“大众”），为每个标签和频谱。 “...”传世到spectrumSel，所以它是可以选择的多肽或蛋白质。
Convenience function, calls reporterData(...,element="ions")
方便的功能，来电reporterData（...，元素=“离子”）
Convenience function, calls reporterData(...,element="mass")
方便的功能，呼吁reporterData（...，元素=“大众”）
Gets the spectrum titles. '...' is passed down to spectrumSel.
获取频谱标题。 “...”通过到spectrumSel。
Gets and sets the class labels in phenoData. Used for summarization, see also estimateRatio and phenoData.
获取和设置在phenoData类的标签。概括使用，也看到estimateRatio和phenoData。
方法----------Methods----------
In the following code snippets, x is a IBSpectra object.
在下面的代码片段，x是IBSpectra对象。
Get a 'subset' of IBSpectra: include or exclude proteins or peptides. When selection is based on proteins, it can be defined to exclude only peptides which are specific to the protein ('reporter-specific'), specific to the group ('group-specific') or
“子集”的IBSpectra：包括或排除蛋白质或多肽。当选择是基于对蛋白质，它可以被定义为排除这是特定的蛋白质（“记者，具体”），特定组（“特定组）或只肽
Gets a boolean vector selecting the corresponding spectra: If peptide is given, all spectra assigned to this peptide. If protein is given, all spectra assigned to peptides of this protein with specificity 'specificity'. See also ProteinGroup.
获取一个布尔向量，选择相应的光谱：如果给出肽，所有光谱分配到这种肽。如果给出了蛋白质，所有光谱分配给这与特异性的特异性蛋白肽。还可以看ProteinGroup。
作者（S）----------Author(s)----------
Florian P. Breitwieser
参见----------See Also----------
ProteinGroup, isobar-preprocessing, isobar-analysis, isobar-plots
ProteinGroup，压线，预处理，压线分析，压线图
举例----------Examples----------
data(ibspiked_set1)
ibspiked_set1
head(reporterIntensities(ibspiked_set1))
head(reporterMasses(ibspiked_set1))
proteinGroup(ibspiked_set1)
isotopeImpurities(ibspiked_set1)
# create new object[创建新的对象]
set.seed(123)
data <- data.frame(spectrum=letters,
peptide=sample(c("pepA","pepB","pepC"),26,TRUE),
accession=c("protein1","protein2"))
data.ions <- matrix(rnorm(26*2,1000,50),
ncol=2,dimnames=list(letters,NULL))
data.mass <- matrix(rep(c(126.1,127.1),26),
ncol=2,byrow=TRUE,dimnames=list(letters,NULL))
ib <- new("TMT2plexSpectra",data,data.ions,data.mass)
ib
reporterIntensities(ib)
isotopeImpurities(ib) <- matrix(c(0.8,0.1,0.2,0.9),nrow=2)
reporterIntensities(correctIsotopeImpurities(ib))
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 22:35:44
