tuneInPeakInfo {MassSpecWavelet}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.

See Also

peakDetectionCWT

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')


[Package MassSpecWavelet version 1.8.0 Index]