xcmsRaw-class(xcms)
xcmsRaw-class()所属R语言包：xcms
Class xcmsRaw, a class for handling raw data
xcmsRaw类，一类用于处理原始数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class handles processing and visualization of the raw data from a single LC/MS or GS/MS run. It includes methods for producing a standard suite of plots including individual spectra, multi-scan average spectra, TIC, and EIC. It will also produce a feature list of significant peaks using matched filtration.
这个类处理从一个单一的LC / MS或GS / MS运行的原始数据的处理和可视化。它包括生产标准套房，包括个人的光谱，平均光谱扫描，议会和EIC图的方法。它也将产生显著峰使用匹配过滤功能列表。
类的对象----------Objects from the Class----------
Objects can be created with the xcmsRaw constructor which reads data from a NetCDF file into a new object.
xcmsRaw从netCDF文件中的数据读入一个新的对象的构造函数可以创建对象。
插槽----------Slots----------
acquisitionNum: acquisitionNum
acquisitionNum：acquisitionNum
environment with three variables: mz - concatenated m/z values for all scans, intensity - corresponding signal intensity for each m/z value, and profile - matrix represention of the intensity values with columns representing scans and rows representing equally spaced m/z values
环境与三个变量：mz - 串联m / z值，所有的扫描，intensity - 每个m / z值相应的信号强度，profile - 强度值的矩阵表示形式列代表代表等距离的m / z值的扫描和行
filepath: Path to the raw data file
filepath：原始数据文件的路径
matrix with first row, time, containing the time point for interpolation and successive columns representing solvent fractions at each point
矩阵的第一行，time，包含插值代表溶剂组分在每一个点的连续列的时间点
msnAcquisitionNum: for each scan a unique acquisition number as reported via "spectrum id" (mzData) or "<scan num=...>" and
msnAcquisitionNum：每次扫描一个独特的收购数量，如通过“频谱ID”（mzData）或“<scan num=...>”和报告
msnCollisionEnergy: "CollisionEnergy" (mzData) or
msnCollisionEnergy：的“CollisionEnergy”（mzData）或
msnLevel: for each scan the "msLevel" (both mzData and mzXML)
msnLevel：为每个扫描的“msLevel”（都mzData和mzXML）
msnPrecursorCharge: "ChargeState" (mzData) and
msnPrecursorCharge：“ChargeState”（mzData）
msnPrecursorIntensity: "Intensity" (mzData) or "precursorIntensity" (mzXML)
msnPrecursorIntensity：“强度”（mzData）或“precursorIntensity”（mzXML的）
msnPrecursorMz: "MassToChargeRatio" (mzData) or
msnPrecursorMz：“MassToChargeRatio”（mzData）
msnPrecursorScan: "spectrumRef" (both mzData and mzXML)
msnPrecursorScan：“spectrumRef”（都mzData和mzXML）
msnRt: Retention time of the scan
msnRt：扫描的保留时间
msnScanindex: msnScanindex
msnScanindex：msnScanindex
numeric vector of length 2 with minimum and maximum m/z values represented in the profile matrix
最小和最大的m / z值在配置矩阵为代表的长度为2的数字矢量
polarity: polarity
polarity：极性
characer value with name of method used for generating the profile matrix
characer值方法名用于生成的文件矩阵
profparam: profparam
profparam：profparam
integer vector with starting positions of each scan in the mz and intensity variables (note that index values are based off a 0 initial position instead of 1)
每次扫描的起始位置的整数向量mz和intensity变量（注意，索引值是基于0的初始位置，而不是1）
numeric vector with acquisition time (in seconds) for each scan
每个扫描数字矢量与采集时间（秒）
numeric vector with total ion count (intensity) for each scan
数字矢量每个扫描总离子数（强度）
方法----------Methods----------
signature(object = "xcmsRaw"): feature detection using matched filtration in the chromatographic time domain
signature(object = "xcmsRaw")：使用色谱时域特征检测匹配过滤
signature(object = "xcmsRaw"): get extracted ion chromatograms in specified m/z ranges
signature(object = "xcmsRaw")：在指定的m / z范围得到提取离子色谱图
signature(object = "xcmsRaw"): get data for peaks in specified m/z and time ranges
signature(object = "xcmsRaw")：在指定的m / z和时间范围峰的数据
signature(object = "xcmsRaw"): get m/z and intensity values for a single mass scan
signature(object = "xcmsRaw")：m / z和强度值，得到一个单一的质量扫描
signature(object = "xcmsRaw"): get average m/z and intensity values for multiple mass scans
signature(object = "xcmsRaw")：平均得到m / z和多个大规模扫描的强度值
signature(x = "xcmsRaw"): get data for peaks in specified m/z and time ranges
signature(x = "xcmsRaw")：在指定的m / z和时间范围峰的数据
signature(object = "xcmsRaw"): plot a chromatogram from profile data
signature(object = "xcmsRaw")：图从配置文件数据的色谱图
signature(object = "xcmsRaw"): plot locations of raw intensity data points
signature(object = "xcmsRaw")：原始强度数据的图位置点
signature(object = "xcmsRaw"): plot a mass spectrum of an individual scan from the raw data
signature(object = "xcmsRaw")：从原始数据绘制一个单独的扫描质谱
signature(object = "xcmsRaw"): plot a mass spectrum from profile data
signature(object = "xcmsRaw")：图从配置数据的质谱
signature(object = "xcmsRaw"): experimental method for plotting 3D surface of profile data with rgl.
signature(object = "xcmsRaw")：图用rgl三维表面轮廓数据的实验方法。
signature(object = "xcmsRaw"): plot total ion count chromatogram
signature(object = "xcmsRaw")：小区总离子数色谱
signature(object = "xcmsRaw"): median filter profile data in time and m/z dimensions
signature(object = "xcmsRaw")：过滤器的个人资料数据，中位数时间和m / z尺寸
signature(object = "xcmsRaw"): change the method of generating the profile matrix
signature(object = "xcmsRaw")：profile矩阵生成方法改变
signature(object = "xcmsRaw"): get the method of generating the profile matrix
signature(object = "xcmsRaw")：生成profile矩阵的方法
signature(object = "xcmsRaw"): get vector of m/z values for each row of the profile matrix
signature(object = "xcmsRaw")：profile矩阵的每一行的m / z值向量
signature(object = "xcmsRaw"): interpret flexible ways of specifying subsets of the profile matrix
signature(object = "xcmsRaw")：解释的指定profile矩阵子集，灵活的方式
signature(object = "xcmsRaw"): change the m/z step used for generating the profile matrix
signature(object = "xcmsRaw")：改变用于生成profile矩阵的m / z一步
signature(object = "xcmsRaw"): get the m/z step used for generating the profile matrix
signature(object = "xcmsRaw")：用于生成profile矩阵的m / z步
signature(object = "xcmsRaw"): reverse the order of the data points for each scan
signature(object = "xcmsRaw")：扭转顺序扫描每个数据点
signature(object = "xcmsRaw"): sort the data points by increasing m/z for each scan
signature(object = "xcmsRaw")：排序增加的m / z为每个扫描数据点
signature(object = "xcmsRaw"): Raw data correction for lock mass calibration gaps.
signature(object = "xcmsRaw")：原始数据的锁质量校准空白校正。
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----------
xcmsRaw
xcmsRaw
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 16:11:30
