MassSpecWavelet (version 1.38.0)

peakDetectionCWT: The main function of peak detection by CWT based pattern matching

Description

This function is a wrapper of cwt, getLocalMaximumCWT, getRidge, identifyMajorPeaks

Usage

peakDetectionCWT(ms, scales = c(1, seq(2, 30, 2), seq(32, 64, 4)), SNR.Th = 3, nearbyPeak = TRUE, peakScaleRange = 5, amp.Th = 0.01, minNoiseLevel = amp.Th/SNR.Th, ridgeLength = 24, peakThr=NULL, tuneIn = FALSE, ...)

Arguments

ms

the mass spectrometry spectrum

scales

scales of CWT

SNR.Th

SNR (Signal to Noise Ratio) threshold

nearbyPeak

Determine whether to include the nearby small peaks of major peaks. TRUE by default

peakScaleRange

the scale range of the peak. larger than 5 by default.

amp.Th

the minimum required relative amplitude of the peak (ratio to the maximum of CWT coefficients)

minNoiseLevel

the minimum noise level used in computing the SNR

ridgeLength

the minimum highest scale of the peak in 2-D CWT coefficient matrix

peakThr

Minimal absolute intensity (above the baseline) of peaks to be picked. If this value is provided, then the smoothing function sav.gol will be called to estimate the local intensity.(added based on the suggestion and code of Steffen Neumann)

tuneIn

determine whether to tune in the parameter estimation of the detected peaks

...

other parameters used by identifyMajorPeaks and smoothing function sav.gol

Value

majorPeakInfo

return of identifyMajorPeaks

ridgeList

return of getRidge

localMax

return of getLocalMaximumCWT

wCoefs

2-D CWT coefficient matrix, see cwt for details.

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.

See Also

cwt, getLocalMaximumCWT, getRidge, identifyMajorPeaks

Examples

	data(exampleMS)
	SNR.Th <- 3
	peakInfo <- peakDetectionCWT(exampleMS, SNR.Th=SNR.Th)
	majorPeakInfo = peakInfo$majorPeakInfo
	peakIndex <- majorPeakInfo$peakIndex
	plotPeak(exampleMS, peakIndex, main=paste('Identified peaks with SNR >', SNR.Th)) 
	
	## In some cases, users may want to add peak filtering based on the absolute peak amplitude
	peakInfo <- peakDetectionCWT(exampleMS, SNR.Th=SNR.Th, peakThr=500)
	majorPeakInfo = peakInfo$majorPeakInfo
	peakIndex <- majorPeakInfo$peakIndex
	plotPeak(exampleMS, peakIndex, main=paste('Identified peaks with SNR >', SNR.Th))