peakDetectionCWT {MassSpecWavelet} | R Documentation |
This function is a wrapper of cwt
, getLocalMaximumCWT
, getRidge
, identifyMajorPeaks
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, ...)
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 |
majorPeakInfo |
return of identifyMajorPeaks |
ridgeList |
return of getRidge |
localMax |
return of getLocalMaximumCWT |
wCoefs |
2-D CWT coefficient matrix, see cwt for details. |
Pan Du, Simon Lin
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.
cwt
, getLocalMaximumCWT
, getRidge
, identifyMajorPeaks
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))