R语言 MassSpecWavelet包 identifyMajorPeaks()函数中文帮助文档(中英文对照)

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identifyMajorPeaks(MassSpecWavelet)
identifyMajorPeaks()所属R语言包：MassSpecWavelet

                                         Identify peaks based on the ridges in 2-D CWT coefficient matrix
                                         确定的2-D小波变换系数矩阵基于脊峰

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Indentify the peaks based on the ridge list (returned by getRidge) in 2-D CWT coefficient matrix and estimated Signal to Noise Ratio (SNR)
增加识别基于脊名单的峰（返回getRidge）的2-D小波变换系数矩阵和估计信号信噪比（SNR）


用法----------Usage----------


identifyMajorPeaks(ms, ridgeList, wCoefs, scales = as.numeric(colnames(wCoefs)), SNR.Th = 3, peakScaleRange = 5, ridgeLength = 32, nearbyPeak = FALSE, nearbyWinSize = 100, winSize.noise = 500, SNR.method = "quantile", minNoiseLevel = 0.001)



参数----------Arguments----------

参数：ms
the mass spectrometry spectrum   
质谱谱


参数：ridgeList
returned by getRidge
返回getRidge


参数：wCoefs
2-D CWT coefficients  
的2-D小波变换系数


参数：scales
scales of CWT, by default it is the colnames of wCoefs  
连续小波变换的尺度，默认情况下它是wCoefs colnames


参数：SNR.Th
threshold of SNR  
信噪比阈值


参数：peakScaleRange
the CWT scale range of the peak.  
CWT的规模范围内的峰值。


参数：ridgeLength
the maximum ridge scale of the major peaks.  
主要山峰最高脊规模。


参数：nearbyPeak
determine whether to include the small peaks close to large major peaks  
确定是否包括大主要山峰附近的小峰


参数：nearbyWinSize
the window size to determine the nearby peaks. Only effective when nearbyPeak is true.
窗口的大小来确定附近的山峰。唯一有效的当nearbyPeak是真实的。


参数：winSize.noise
the local window size to estimate the noise level.  
本地窗口的大小来估计噪音水平。


参数：SNR.method
method to estimate noise level. Currently, only 95 percentage quantile is supported.  
估计噪音水平的方法。目前，只有95个位数的支持。


参数：minNoiseLevel
the minimum noise level used in calculating SNR, i.e., if the estimated noise level is less than "minNoiseLevel", it will use "minNoiseLevel" instead. If the noise level is less than 0.5, it will be treated as the ratio to the maximum amplitude of the spectrum.  
用于计算信噪比的最低噪音水平，也就是说，如果估计的噪音水平是比“minNoiseLevel”，它会使用“minNoiseLevel”代替。如果噪音水平小于0.5，将被视为对频谱的最大振幅的比率。


Details

详情----------Details----------

The determination of the peaks is based on three rules: Rule 1: The maximum ridge scale of the peak should larger than a certain threshold Rule 2: Based on the scale of the peak (corresponding to the maximum value of the peak ridge) should be within certain range Rule 3: Based on the peak SNR
峰的决心，是基于三个规则：规则1：最大的高峰期应大于某一阈值第2大垄规模：基于规模的峰值（对应的峰脊的最高值），应该在一定范围内第3条：基于峰值信噪比


值----------Value----------

Return a list with following elements:
返回与以下元素的一个列表：


参数：peakIndex
the m/z indexes of the identified peaks
确定峰的m / z指数


参数：peakCenterIndex
the m/z indexes of peak centers, which correspond to the maximum on the ridge. peakCenterIndex includes all the peaks, not just the identified major peaks.
峰中心的m / z索引，对应于垄上最大的。 peakCenterIndex包括所有的高峰，而不是刚刚确定的主要山峰。


参数：peakCenterValue
the CWT coefficients (the maximum on the ridge) corresponding to peakCenterIndex
小波变换系数（脊最大）相应peakCenterIndex的


参数：peakSNR
the SNR of the peak, which is the ratio of peakCenterValue  and noise level
峰值信噪比，这是的peakCenterValue和噪音水平比


参数：peakScale
the estimated scale of the peak, which corresponds to the peakCenerIndex
峰值的估计规模，对应的peakCenerIndex


参数：potentialPeakIndex
the m/z indexes of all potential peaks, which satisfy all requirements of a peak without considering its SNR. Useful, if you want to change to a lower SNR threshold later.
所有潜在的峰的m / z索引，满足高峰的所有要求，而不考虑其信噪比。有用，如果你想改变到一个较低的信噪比门限。


参数：allPeakIndex
the m/z indexes of all the peaks, whose order is the same as peakCenterIndex, peakCenterValue, peakSNR and peakScale.
所有峰的m / z索引，其顺序是作为peakCenterIndex，peakCenterValue，peakSNR和peakScale相同。

All of these return elements have peak names, which are the same as the corresponding peak ridges. see getRidge for details.
所有这些返回元素峰的名字，这是相应的峰脊。看到getRidge详情。


作者（S）----------Author(s)----------


Pan Du, Simon Lin



参考文献----------References----------



参见----------See Also----------

peakDetectionCWT, tuneInPeakInfo
peakDetectionCWT，tuneInPeakInfo


举例----------Examples----------


        data(exampleMS)
        scales <- seq(1, 64, 3)
        wCoefs <- cwt(exampleMS, scales=scales, wavelet='mexh')
       
        localMax <- getLocalMaximumCWT(wCoefs)
        ridgeList <- getRidge(localMax)
       
        SNR.Th <- 3
        majorPeakInfo <- identifyMajorPeaks(exampleMS, ridgeList, wCoefs, SNR.Th=SNR.Th)
        ## Plot the identified peaks[＃绘制确定峰]
        peakIndex <- majorPeakInfo$peakIndex
        plotPeak(exampleMS, peakIndex, main=paste('Identified peaks with SNR >', SNR.Th))
       

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


注：
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