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

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xcmsSet-class(xcms)
xcmsSet-class()所属R语言包：xcms

                                        Class xcmsSet, a class for preprocessing peak data
                                         xcmsSet类，一类为预处理的峰值数据

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This class transforms a set of peaks from multiple LC/MS or GC/MS samples into a matrix of preprocessed data. It groups the peaks and does nonlinear retention time correction without internal standards. It fills in missing peak values from raw data. Lastly, it generates extracted ion chromatograms for ions of interest.
这个类转换从多个LC / MS或GC / MS分析样品预处理后的数据矩阵的一组峰。这组峰和非线性的保留时间校正不需要的内部标准。它填补了缺少原始数据的峰值。最后，它产生兴趣离子的提取离子色谱。


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

Objects can be created with the xcmsSet constructor which gathers peaks from a set NetCDF files. Objects can also be created by calls of the form new("xcmsSet", ...).
对象可以创建xcmsSet构造一套NetCDF文件集的高峰。对象也可以通过检测的形式new("xcmsSet", ...)创建。


插槽----------Slots----------

matrix containing peak data
矩阵包含的峰值数据

a vector with peak indices of peaks which have been added by a fillPeaks method,
向量的已fillPeaks方法的增加峰峰值指数，

matrix containing statistics about peak groups
矩阵包含峰集团的统计，大约有

list containing indices of peaks in each group
峰，在各组的列表，包含指数

a data frame containing the experimental design factors
一个数据框包含的实验设计因素

list containing two lists, raw and corrected, each containing retention times for every scan of every sample
列表，其中包含两个列表，raw和corrected，每个每个每个样品扫描含保留时间

character vector with absolute path name of each NetCDF file
特征向量与每个netCDF文件的绝对路径名

list containing two values, method - profile generation method, and step - profile m/z step size
列表，其中包含两个值，method - 配置文件的生成方法，并step - 个人资料的m / z步长

logical vector filled if the waters Lock mass correction  parameter is used.   
充满逻辑向量水域锁定如果使用质量校正参数。

a string ("positive" or "negative" or NULL) describing whether only positive or negative scans have been used reading the raw data.
字符串（“积极”或“负”或NULL），说明是否已被用于读取原始数据只有积极或消极的扫描。

progress informations for some xcms functions (for GUI)
进度信息一些xcms功能（用于GUI）

function to be called, when progressInfo changes (for GUI)
功能被调用时，progressInfo变化（GUI），


方法----------Methods----------

signature("xcmsSet"): combine objects together
signature("xcmsSet")：结合对象

signature(object = "xcmsSet"): set filepaths slot
signature(object = "xcmsSet")：filepaths插槽

signature(object = "xcmsSet"): get filepaths slot
signature(object = "xcmsSet")：得到filepaths插槽

signature(object = "xcmsSet"): create report of differentially regulated ions including EICs
signature(object = "xcmsSet")：创造差异调节离子，包括EICs报告

signature(object = "xcmsSet"): fill in peak data for groups with missing peaks
signature(object = "xcmsSet")：填写组的峰值数据丢失峰

signature(object = "xcmsSet"): get list of EICs for each sample in the set
signature(object = "xcmsSet")：让每个样品中集的EICs名单

signature(object = "xcmsSet"): set groupidx slot
signature(object = "xcmsSet")：groupidx插槽

signature(object = "xcmsSet"): get groupidx slot
signature(object = "xcmsSet")：得到groupidx插槽

signature(object = "xcmsSet"): get textual names for peak groups
signature(object = "xcmsSet")：高峰组文本名称

signature(object = "xcmsSet"): set groups slot
signature(object = "xcmsSet")：groups插槽

signature(object = "xcmsSet"): get groups slot
signature(object = "xcmsSet")：得到groups插槽

signature(object = "xcmsSet"): get matrix of values from peak data with a row for each peak group
signature(object = "xcmsSet")：峰值数据行的值矩阵得到每个峰组

signature(object = "xcmsSet"): find groups of peaks across samples that share similar m/z and retention times
signature(object = "xcmsSet")：找到共享类似的m / z和保留时间的跨样本峰组

signature(object = "xcmsSet"): set peaks slot
signature(object = "xcmsSet")：peaks插槽

signature(object = "xcmsSet"): get peaks slot
signature(object = "xcmsSet")：得到peaks插槽

signature(object = "xcmsSet"): plot retention time deviation profiles
signature(object = "xcmsSet")：图的保留时间偏差概况

signature(object = "xcmsSet"): set profinfo slot
signature(object = "xcmsSet")：profinfo插槽

signature(object = "xcmsSet"): get profinfo slot
signature(object = "xcmsSet")：得到profinfo插槽

signature(object = "xcmsSet"): use initial grouping of peaks to do nonlinear loess retention time correction
signature(object = "xcmsSet")：使用峰的初始分组做非线性黄土的保留时间校正

signature(object = "xcmsSet"): <STRONG>DEPRECATED</STRONG>. If used, the experimental design will be replaced with a data frame with a single column matching the supplied factor.
signature(object = "xcmsSet")：<STRONG>已过时</ STRONG>。如果使用，实验设计，将被替换为一个单一的配套提供的因素列的数据框。

signature(object = "xcmsSet"): get the interaction of the experimental design factors
signature(object = "xcmsSet")：得到的实验设计因素的相互作用

signature(object = "xcmsSet"): set the phenoData slot
signature(object = "xcmsSet")：设置phenoData插槽

signature(object = "xcmsSet"): get the phenoData slot
signature(object = "xcmsSet")：phenoData插槽

signature(object = "xcmsSet"): set the progressCallback slot
signature(object = "xcmsSet")：设置progressCallback插槽

signature(object = "xcmsSet"): get the progressCallback slot
signature(object = "xcmsSet")：progressCallback插槽

signature(object = "xcmsSet"): set rownames in the phenoData slot
signature(object = "xcmsSet")：设置rownames的phenoData插槽

signature(object = "xcmsSet"): get rownames in the phenoData slot
signature(object = "xcmsSet")：phenoData插槽rownames

signature("xcmsSet"): divide into a list of objects
signature("xcmsSet")：分成一个对象列表


注意----------Note----------

No notes yet.
还没有注意到。


作者（S）----------Author(s)----------


Colin A. Smith, <a href="mailto:csmith@scripps.edu">csmith@scripps.edu</a>



参考文献----------References----------

http://metlin.scripps.edu/

参见----------See Also----------

xcmsSet
xcmsSet

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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