NetCDFPeakFinding(TargetSearch)
NetCDFPeakFinding()所属R语言包：TargetSearch
Peak picking algorithm from CDF files
CDF文件山顶采摘算法
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function reads a netcdf chromatogram file, finds the apex intensities and returns a list containing the retention time and the intensity matrices.
此功能读取NetCDF的色谱文件，发现心尖强度，并返回一个列表，其中包含的保留时间和强度矩阵。
用法----------Usage----------
NetCDFPeakFinding(cdfFile, massRange = c(85, 500), Window = 5, IntThreshold = 10,
pp.method = "ppc", baseline = FALSE, baseline.opts = NULL)
参数----------Arguments----------
参数：cdfFile
A character string naming a netcdf file.
一个字符串，命名netCDF文件。
参数：massRange
A two component numeric vector with the scan mass range to extract.
两元件数值向量与扫描质量范围内提取。
参数：Window
The window used by peak picking method. The number of points actually used is 2*Window + 1.
窗口使用高峰期采摘方法。实际使用的点数是2*Window + 1。
参数：IntThreshold
Apex intensities lower than this value will be removed from the RI files.
从RI文件将被删除顶点强度低于此值。
参数：pp.method
The pick picking method to be used. Options are "smoothing" and "ppc".
挑采摘方法可以使用。选项是"smoothing"和"ppc"。
参数：baseline
Logical. Should baseline correction be performed?
逻辑。应进行基线校正？
参数：baseline.opts
A list of options passed to baselineCorrection </table>
一个传递给baselineCorrection</ TABLE>的奖励。选项列表
Details
详情----------Details----------
The function expects the following NetCDF variables: intensity_values, mass_values, scan_index, point_count and scan_acquisition_time. Otherwise, an error will be displayed.
该功能预计以下NetCDF的变量：intensity_values，mass_values，scan_index，point_count和scan_acquisition_time。否则，将显示一个错误。
The massRange parameter is a numeric vector with two components: lower and higher masses. All masses in that range will be extracted. Note that it is not possible to extract a discontinuous mass range.
massRange参数是一个数字矢量两部分组成：较低和较高的群众。在这个范围内的所有群众将被提取。请注意，这是不可能的提取不连续的质量范围。
There are two peak picking algorithms that can be used. The "smoothing" method smooths the m/z curves and then looks for a change of sign of the intensity difference between two consecutive points. The "ppc" uses a sliding window and looks for the local maxima. This method is based on R-package ppc.
有两个高峰期的算法，可用于采摘。 "smoothing"方法平滑的m / z曲线，然后寻找改变连续两个点之间的强度差的迹象。 "ppc"使用一个滑动窗口和局部极大。此方法的基础上的R套件ppc。
值----------Value----------
A two component list.
两元件列表。
参数：Time
The retention time vector.
保留时间的向量。
参数：Peaks
The intensity matrix. Rows are the retention times and columns are masses. The first column is the lower mass value and the last one is the higher mass.
强度矩阵。行的保留时间和列是群众。第一列是低质量的价值，最后一个是更高的质量。
作者（S）----------Author(s)----------
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
参见----------See Also----------
peakCDFextraction
peakCDFextraction
举例----------Examples----------
require(TargetSearchData)
data(TargetSearchData)
CDFpath <- file.path(.find.package("TargetSearchData"), "gc-ms-data")
CDFfiles <- dir(CDFpath, pattern = ".cdf$", full.names = TRUE)
CDFfiles
# extrac peaks of first chromatogram[萃取第一色谱峰]
peaks.1 <- NetCDFPeakFinding(CDFfiles[1], massRange = c(85, 320), Window = 15,
IntThreshold = 10, pp.method = "smoothing")
# scan acquisition times[扫描采集时间]
head(peaks.1$Time)
# peaks in matrix form. first column is mass 85, last one is mass 320.[在矩阵形式的山峰。第一列是质量85，最后一个是群众320。]
head(peaks.1$Peaks)
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 15:22:54
