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

In zeehio/MassSpecWavelet: Peak Detection for Mass Spectrometry data using wavelet-based algorithms

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")

zeehio/MassSpecWavelet documentation built on May 6, 2023, 1:32 a.m.