plotMzDelta-methods(MSnbase)
plotMzDelta-methods()所属R语言包：MSnbase
The delta m/z plot for 'MSnExp' quality assessment
Delta的m / z积“MSnExp质量评估
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The m/z delta plot illustrates the suitability of MS2 spectra for identification by plotting the m/z differences of the most intense peaks. The resulting histogram should optimally shown outstanding bars at amino acid residu masses. The plots have been described in Foster et al 2011.
的m / zDelta图策划最激烈峰的m / z差异的适用性说明MS2的光谱鉴定。由此产生的直方图应最佳氨基酸残差群众突出的条形。图已在2011年Foster等。
Only a certain percentage of most intense MS2 peaks are taken into account to use the most significant signal. Default value is 10% (see percentage argument). The difference between peaks is then computed for all individual spectra and their distribution is plotted as a histogram where single bars represent 1 m/z differences. Delta m/z between 40 and 200 are plotted by default, to encompass the residue masses of all amino acids and several common contaminants, although this can be changes with the xlim argument.
只有一定比例的最激烈的MS2峰考虑使用最显着的信号。默认值是10％（见percentage参数）。峰之间的区别，然后计算所有个别光谱和其分布直方图绘制单条代表1的m / z的差异。默认情况下，Delta的m / z 40和200之间绘制，包括所有的氨基酸和几种常见的污染物残留群众，尽管这可能是参数变化与xlim。
In addition to the processing described above, isobaric reporter tag peaks (see the reporters argument) and the precursor peak (see the precMz argument) can also be removed from the MS2 spectrum, to avoid interence with the fragment peaks.
除了加工中的描述上面，记者等压标记峰（见reporters参数）及易制毒化学峰（见precMz参数），也可以从MS2的频谱中删除，以避免与interence碎片峰。
Note that figures in Foster et al 2011 have been produced and optimised for centroided data. Application of the plot as is for data in profile mode has not been tested thoroughly, although the example below suggest that it might work.
请注意，在2011年Foster等数字已生产和优化centroided数据。图中的应用是在情景模式中的数据并没有被彻底测试，虽然下面的例子表明，它可能会奏效。
The methods make use the ggplot2 system. An object of class 'ggplot' is returned invisibly.
该方法使使用ggplot2系统。返回无形一个类的ggplot“的对象。
Most of the code for plotMzDelta has kindly been contributed by Guangchuang Yu.
大部分代码plotMzDelta好心被，贡献Guangchuang羽。
参数----------Arguments----------
参数：object
An object of class "MSnExp" containing MS2 spectra.
一个对象的类"MSnExp"含MS2的光谱。
参数：reporters
An object of class class "ReporterIons" that defines which reporter ion peaks to set to 0. The default value NULL leaves the spectra as they are.
类的类对象"ReporterIons"定义记者离子峰设置为0。默认值NULL离开，因为它们的光谱。
参数：percentage
The percentage of most intense peaks to be used for the plot. Default is 0.1.
用于图的最激烈的峰的百分比。默认值是0.1。
参数：precMz
A numeric of length one or NULL default. In the latter (and preferred) case, the precursor m/z values are extracted from the individual MS2 spectra using the precursorMz method.
一个numeric长度为一个或NULL默认。在后者的情况下（首选），易制毒化学从个人MS2的使用的precursorMz方法光谱中提取m / z值。
参数：precMzWidth
A numeric of length 1 that specifies the width around the precursor m/z where peaks are set to 0. Default is 2.
一个长度为1numeric指定左右宽度为m / z峰均设置为0的前兆。默认值是2。
参数：bw
A numeric specifying the bandwith to be used to bin the delta m/z value to plot the histogram. Default if 1. See geom_histogram for more details.
一个numeric指定的带宽被用来斌Deltam / z值来绘制直方图。默认情况下，如果1。看到geom_histogram更多细节。
参数：xlim
A numeric of length 2 specifying the range of delta m/z to plot on the histogram. Default is c(40,200).
一个numeric长度为2指定Delta范围内的m / z绘制直方图。默认c(40,200)。
参数：withLabels
A logical defining if amino acid residue labels are plotted on the figure. Default is TRUE.
一个logical界定，如果氨基酸残基的标签上图的绘制。默认TRUE。
参数：size
A numeric of length 1 specifying the font size of amino acids lables. Default is 2.5.
一个长度为1numeric指定字体大小的标贴氨基酸。默认值是2.5。
参数：plot
A numeric of length 1 that defines whether the figure should be plotted on the active device. Default is TRUE. Note that the ggplot object is always returned invisibly.
一个numeric长度为1，定义该数字是否应绘制有源器件。默认TRUE。注意ggplot对象总是返回看不见。
参数：verbose
A logical of length 1 specifying whether textual output and a progress bar illustration the progress of data processing should be printed. Default is TRUE
一个长度为1logical指定文本输出和一个进度条，插图是否应印数据处理的进展。默认是TRUE
方法----------Methods----------
Plots a (invisibly) returns the m/z delta histogram.
图（不可见）返回的m / zDelta直方图。
作者（S）----------Author(s)----------
Laurent Gatto <lg390@cam.ac.uk>
参考文献----------References----------
Martens L. "A posteriori quality control for the curation and reuse of public proteomics data." Proteomics, 2011 Jun;11(11):2182-94. doi:10.1002/pmic.201000602. Epub 2011 May 2. PMID: 21538885
参见----------See Also----------
The plotDensity and plot2d methods for other QC plots.
plotDensity和plot2d其他质控图的方法。
举例----------Examples----------
mzdplot <- plotMzDelta(itraqdata,reporters=iTRAQ4,verbose=FALSE,plot=FALSE)
## let's retrieve peptide sequence information[＃让我们的检索肽序列信息]
## and get a table of amino acids[＃和氨基酸表]
peps <- as.character(fData(itraqdata)$PeptideSequence)
aas <- unlist(strsplit(peps,""))
## table of aas[＃原子吸收光谱法表]
table(aas)
## mzDelta plot[＃mzDelta图]
print(mzdplot)
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 2012-2-26 07:30:56
