peakDetectionCWT {MassSpecWavelet}R Documentation

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, 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 amplitude of the peak
minNoiseLevel the minimum noise level used in computing the SNR
ridgeLength the minimum highest scale of the peak in 2-D CWT coefficient matrix
tuneIn determine whether to tune in the parameter estimation of the detected peaks
... other parameters of used by getLocalMaximumCWT, getRidge, identifyMajorPeaks

Value

majorPeakInfo return of identifyMajorPeaks
ridgeList return of getRidge
localMax return of getLocalMaximumCWT
wCoefs

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

Author(s)

Pan Du, Simon Lin

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)) 

[Package MassSpecWavelet version 1.4.0 Index]