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

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

                                        The 'MSnExp' Class for MS Data And Meta-Data
                                         MSnExp“MS数据和元数据类

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

The MSnExp class encapsulates data and meta-data for mass spectrometry experiments, as described in the slots section. Several data files (currently in mzXML) can be loaded together with the function readMSData.
MSnExp类封装的质谱实验数据和元数据，如在slots节所述。几个数据文件（目前在mzXML）可装载功能readMSData。

This class extends the virtual "pSet" class.
这个类扩展虚拟"pSet"类。


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

Objects can be created by calls of the form new("MSnExp",...). However, it is preferred to use the readMSData function that will read raw mass spectrometry data to generate a valid "MSnExp" instance.
创建对象可以通过检测的形式new("MSnExp",...)。然而，它是首选使用readMSData的功能，将读取原始质谱数据生成一个有效的"MSnExp"实例。


插槽----------Slots----------




assayData: Object of class "environment" containing the MS spectra (see "Spectrum1" and "Spectrum2").
assayData：Object类的"environment"包含质谱（见"Spectrum1"和"Spectrum2"）。




phenoData: Object of class "AnnotatedDataFrame" containing  experimenter-supplied variables describing sample (i.e the individual tags for an labelled MS experiment) See phenoData for more details.
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）见phenoData更多细节。




featureData: Object of class "AnnotatedDataFrame" containing variables describing features (spectra in our case), e.g. identificaiton data, peptide sequence, identification score,... (inherited from "eSet"). See featureData for more details.
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"继承）。看到featureData更多细节。




experimentData: Object of class "MIAPE", containing details of experimental methods. See experimentData for more details.
experimentData类"MIAPE"，包含实验方法的细节的对象。看到experimentData更多细节。




protocolData: Object of class "AnnotatedDataFrame" containing equipment-generated variables (inherited from "eSet"). See protocolData for more details.
protocolData类"AnnotatedDataFrame"包含设备生成的变量（从"eSet"继承）的对象。看到protocolData更多细节。




processingData: Object of class "MSnProcess" that records all processing.
processingData类"MSnProcess"的记录对象的所有处理。




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


延伸----------Extends----------

Class "pSet", directly. Class "VersionedBiobase", by class "pSet", distance 2. Class "Versioned", by class "pSet", distance 3.
类"pSet"，直接。类"VersionedBiobase"，一流“的pset”，距离为2。类"Versioned"，一流“的pset”，距离3。


方法----------Methods----------

See the "pSet" class for documentation on  accessors inherited from pSet, subsetting and general attribute accession.
见"pSet"的文件存取类继承pSet，子集和一般属性加入。




clean signature(object = "MSnExp"): Removes unused 0 intensity data points. See clean documentation
清洁signature(object = "MSnExp")：移除未使用0强度数据点。见clean文件




extractPrecSpectra signature(object = "MSnExp", prec =         "numeric"): extracts spectra with precursor MZ value equal to prec and returns an object of class 'MSnExp'. See extractPrecSpectra documentation for more
extractPrecSpectrasignature(object = "MSnExp", prec =         "numeric")：易制毒化学，锰锌价值相当于prec提取光谱和返回一个类的MSnExp的对象。看到更多的extractPrecSpectra文件




extractSpectra signature(object = "MSnExp", selected =         "logical"): extracts spectra corresponding to 'TRUE' in selected. See extractSpectra documentation for more details
extractSpectrasignature(object = "MSnExp", selected =         "logical")：光谱中提取相应的真selected。详情请参阅extractSpectra文件




plot signature(x = "MSnExp", y = "missing"): Plots all the spectra of the MSnExp instance. See
图signature(x = "MSnExp", y = "missing")：绘制所有的光谱MSnExp实例。见




plot2d signature(object = "MSnExp", ...): Plots retention time against precursor MZ for MSnExp instances. See plot2d documentation for more
plot2dsignature(object = "MSnExp", ...)：图MSnExp实例，对易制毒化学锰锌滞留时间。看到更多的plot2d文件




plotDensity signature(object = "MSnExp", ...): Plots the density of parameters of interest.       instances. See plotDensity documentation for more
plotDensitysignature(object = "MSnExp", ...)：图感兴趣的参数的密度。实例。看到更多的plotDensity文件




plotMzDelta signature(object = "MSnExp", ...): Plots a histogram of the m/z difference betwee all of the highest peaks of all MS2 spectra of an experiment.
plotMzDeltasignature(object = "MSnExp", ...)：绘制直方图的m / z区别betwee MS2的所有实验光谱的最高峰。




quantify signature(object = "MSnExp"): Performs quantification for all the MS2 spectra of the MSnExp instance. See quantify documentation for more
量化signature(object = "MSnExp")：执行所有的MS2MSnExp实例光谱定量分析。看到更多的quantify文件




removePeaks signature(object = "MSnExp"): Removes peaks lower that a threshold t. See removePeaks documentation for more details and
removePeakssignature(object = "MSnExp")：删除峰较低的阈值t。见removePeaks更多细节文件和




removeReporters signature(object = "MSnExp", ...): Removes reporter ion peaks from all MS2 spectra of an experiment. See removeReporters documentation for
removeReporterssignature(object = "MSnExp", ...)：删除所有MS2的实验光谱记者离子峰。 removeReporters文件




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




trimMz signature(object = "MSnExp"): Trims the MZ range of all the spectra of the MSnExp instance. See trimMz documentation for more details and
trimMzsignature(object = "MSnExp")：花边所有MSnExp实例光谱的锰锌范围。见trimMz更多细节文件和


作者（S）----------Author(s)----------



Laurent Gatto <lg390@cam.ac.uk>




参考文献----------References----------

specific formats to mzXML: http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML.

参见----------See Also----------

"pSet" and readMSData for loading mzXML, mzData or mzML files to generate an instance of MSnExp.
"pSet"和readMSData加载mzXML，mzData或mzML文件生成一个MSnExp的实例。


举例----------Examples----------


mzxmlfile <- dir(system.file("extdata",package="MSnbase"),
                 pattern="mzXML",full.names=TRUE)
msnexp <- readMSData(mzxmlfile)
msnexp

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