quantify-methods(MSnbase)
quantify-methods()所属R语言包：MSnbase
Quantifies 'MSnExp' and 'Spectrum' objects
量化“MSnExp和谱的对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This method quantifies individual "Spectrum" objects or full "MSnExp" experiments. Current implementation quantify specific peaks in individual spectra. The peaks of interest are defined by the reporters parameter using one of the possible method methods. This essentially qualifies for MSMS quantitation using isobaric tags, altough any peak can be defined in reporters.
这种方法量化个人"Spectrum"对象或全"MSnExp"实验。目前实施量化具体个别光谱峰。感兴趣的峰reporters使用可能method的方法之一参数定义。这实质上是环境科学使用等压标记的定量的资格，虽然任何峰可以被定义在reporters。
参数----------Arguments----------
参数：object
Objects of class "Spectrum" or "MSnExp".
对象的类"Spectrum"或"MSnExp"。
参数：method
Peak quantitation method. One of, possibly abreviated "trapezoidation", "max", or "sum". These methods return respectively the area under the peak(s), the maximum of the peak(s) or the sum of all intensities of the peak(s).
山顶的定量方法。一，可能是缩写“trapezoidation”，“最大”，或“总和”。这些方法分别返回下峰面积（S），最大峰值（S）或峰值（S）的所有强度的总和。
参数：reporters
An object of class "ReporterIons" that defines the peak(s) to be quantified.
一个类的对象"ReporterIons"定义量化的峰值（S）。
参数：strict
If strict is 'FALSE' (default), the quantitation is performed using data points along the entire width of a peak. If strict is set to 'TRUE', once the apex(es) is/are identified, only data points within apex +/- width of reporter (see "ReporterIons") are used for quantitation.
如果严格为“假”（默认），定量分析使用的数据点，沿整个宽度的一个高峰。如果严格设置为“TRUE”，一旦APEX（ES）是/确定，仅先端内的数据点+ / - 记者宽度（见"ReporterIons"）用于定量。
参数：verbose
Verbose of the output (only for MSnExp objects).
详细输出（只适用于MSnExp对象）。
Details
详情----------Details----------
"ReporterIons" define specific MZ at which peaks are expected and a window around that MZ value. A peak of interest is searched for in that window. Since version 1.1.2, warnings are not thrown anymore in case no data is found in that region or if the peak extends outside the window. This can be checked manually after quantitation, by inspecting the quantitation data (using the exprs accessor) for NA values or by comaring the lowerMz and upperMz columns in the "MSnSet" qual slot against the respective expected mz(reporters) +/- width(reporters). This is illustrated in the example below.
"ReporterIons"定义特定的锰锌峰预计左右，锰锌价值的窗口。在该窗口中搜索感兴趣的一个高峰。自1.1.2版本起，警告不抛出了没有数据的情况下被发现在该区域或高峰窗外延伸。这可以手动检查，定量分析后，通过检查exprs值的定量数据（NA存取）或由comaring<lowerMz和upperMz列X>"MSnSet"插槽对各自的预期qual+ / - mz(reporters)。在下面的例子说明了这一点。
Once the range of the curve is found, quantification is performed. If no data points are found in the expected region, 'NA' is returned for the reporter peak MZ.
一旦被发现，曲线的范围进行量化。如果没有数据点在预期的区域发现，“不适用”记者高峰锰锌返回。
方法----------Methods----------
Quantifies peaks defined in reporters using method in all spectra of the MSnExp object. If verbose is set to TRUE, a progress bar will be displayed.
量化reporters使用的定义峰method所有光谱MSnExp对象。如果详细的设置TRUE，将显示一个进度栏。
An object of class "MSnSet" is returned containing the quantified feature expression and all meta data inherited from the MSnExp argument.
"MSnSet"类的对象，则返回包含量化的功能表达和继承MSnExp参数的所有元数据。
Quantifies peaks defined in reporters using method in the Spectrum object.
量化reporters使用methodSpectrum对象的定义的高峰。
A list of length 2 will be returned. The first element, named peakQuant, is a 'numeric' of length equal to length(reporters) with quantitation of the reporter peaks using method.
名单将返回一个长度为2。第一个元素，名为peakQuant，是一个“数字”使用length(reporters)method记者峰定量的长度等于。
The second element, names curveStats, is a 'data.frame' of dimension length(reporters) times 7 giving, for each reporter curve parameters: maximum intensity ('maxInt'), number of maxima ('nMaxInt'), number of data points defined the curve ('baseLength'), lower and upper MZ values for the curve ('lowerMz' and 'upperMz'), reporter ('reporter') and precursor MZ value ('precursor') when available.
第二个元素，名称curveStats，是一个“数据框”维length(reporters)7倍，给每个记者曲线参数：最大强度（MAXINT“），极大的数（nMaxInt时），数量的数据点定义的曲线（baseLength）曲线（lowerMz和upperMz），记者（记者）及易制毒化学锰锌值的下限和上限的的锰锌值（前兆） 。
作者（S）----------Author(s)----------
Laurent Gatto <lg390@cam.ac.uk>
举例----------Examples----------
## quantifying full experiment[＃量化充分的实验]
file <- dir(system.file(package="MSnbase",dir="extdata"),full.name=TRUE,pattern="mzXML$")
aa <- readMSData(file,verbose=FALSE)
msnset <- quantify(aa,method="trap",reporters=iTRAQ4)
msnset
## checking for non-quantified peaks[＃检查非量化峰的]
sum(is.na(exprs(msnset)))
## checking for peaks outside of first reporter width[＃检查以外的第一次记者宽度为峰]
lowerMz.114 <- qual(msnset)$lowerMz[qual(msnset)$reporter=="114.1"]
upperMz.114 <- qual(msnset)$upperMz[qual(msnset)$reporter=="114.1"]
any(lowerMz.114 < mz(iTRAQ4[1]) - width(iTRAQ4[1]))
any(upperMz.114 > mz(iTRAQ4[1]) + width(iTRAQ4[1]))
## quantifying single spectrum[＃量化单频谱]
qty <- quantify(aa[[1]],method="trap",iTRAQ4[1])
qty$peakQuant
qty$curveStats
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。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
|
发表于 2012-2-26 07:31:36
