findPeaks.MSW-methods {xcms} | R Documentation |
Processing Mass Spectrometry direct-injection spectrum by using wavelet based algorithm.
object |
xcmsSet object |
snthresh |
signal to noise ratio cutoff |
scales |
scales of CWT |
nearbyPeak |
Determine whether to include the nearby small peaks of major peaks. TRUE by default |
sleep |
number of seconds to pause between plotting peak finding cycles |
verbose.columns |
additional peak meta data columns are returned |
This is a wrapper around the peak picker in the bioconductor package MassSpecWavelet calling 'cwt', 'get.localMaximum.cwt', 'get.ridge', 'identify.majorPeaks' and tuneIn.peakInfo.
A matrix with columns:
mz |
weighted (by intensity) mean of peak m/z across scans |
mzmin |
same as mz |
mzmax |
same as mz |
rt |
always -1 |
rtmin |
always -1 |
rtmax |
always -1 |
into |
integrated area of original (raw) peak |
maxo |
intensity of original (raw) peak at the centroid position |
sn |
Signal/Noise ratio |
findPeaks.MSW(object, snthresh=3,
scales=seq(1,22,3), nearbyPeak=TRUE,
peakScaleRange=5, amp.Th=0.01,
minNoiseLevel=amp.Th/SNR.Th,
ridgeLength=24, tuneIn=FALSE,
sleep=0, verbose.columns = FALSE)
Steffen Neumann, sneumann@ipb-halle.de
findPeaks-methods
xcmsRaw-class