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Last data update: 2014.03.03

R: Tune in the peak information: peak position and peak scale

tuneInPeakInfo

R Documentation

Tune in the peak information: peak position and peak scale

Description

Based on the identified peak position, more precise estimation of the peak information, i.e., peak position and peak scale, can be got by this function. The basic idea is to cut the segment of spectrum near the identified peaks, and then do similar procedures as peakDetectionCWT, but with more detailed scales around the estimated peak scale.

Usage

tuneInPeakInfo(ms, majorPeakInfo = NULL, peakIndex = NULL, peakScale = NULL, maxScale = 128, ...)

Arguments

`ms`	the mass spectrometry spectrum
`majorPeakInfo`	return of `identifyMajorPeaks`
`peakIndex`	the m/z index of the identified peaks
`peakScale`	the scales of the identified peaks
`maxScale`	the maximum scale allowed for the peak
`...`	other parameters of used by `getLocalMaximumCWT`, `getRidge`, `identifyMajorPeaks`

Details

The majorPeakInfo or peakIndex and peakScale must be provided.

Value

`peakCenterIndex`	the updated peak center m/z index
`peakScale`	the updated peak scale
`peakValue`	the corresponding peak value

Author(s)

Pan Du

References

Du, P., Kibbe, W.A. and Lin, S.M. (2006) Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching, Bioinformatics, 22, 2059-2065.

Examples


	data(exampleMS)
	SNR.Th <- 3
	peakInfo <- peakDetectionCWT(exampleMS, SNR.Th=SNR.Th)
	majorPeakInfo <- peakInfo$majorPeakInfo
	betterPeakInfo <- tuneInPeakInfo(exampleMS, majorPeakInfo)
	plot(500:length(exampleMS), exampleMS[500:length(exampleMS)], type='l', log='x')
	abline(v=betterPeakInfo$peakCenterIndex, col='red')

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(MassSpecWavelet)
Loading required package: waveslim

waveslim: Wavelet Method for 1/2/3D Signals (version = 1.7.5)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MassSpecWavelet/tuneInPeakInfo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: tuneInPeakInfo
> ### Title: Tune in the peak information: peak position and peak scale
> ### Aliases: tuneInPeakInfo
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> 	data(exampleMS)
> 	SNR.Th <- 3
> 	peakInfo <- peakDetectionCWT(exampleMS, SNR.Th=SNR.Th)
> 	majorPeakInfo <- peakInfo$majorPeakInfo
> 	betterPeakInfo <- tuneInPeakInfo(exampleMS, majorPeakInfo)
> 	plot(500:length(exampleMS), exampleMS[500:length(exampleMS)], type='l', log='x')
> 	abline(v=betterPeakInfo$peakCenterIndex, col='red')
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>