findPeaks.MSW-methods {xcms}R Documentation

Feature detection for single-spectrum non-chromatography MS data

Description

Processing Mass Spectrometry direct-injection spectrum by using wavelet based algorithm.

Arguments

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

Details

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.

Value

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

Methods

object = "xcmsRaw"
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)

Author(s)

Steffen Neumann, sneumann@ipb-halle.de

See Also

findPeaks-methods xcmsRaw-class


[Package xcms version 1.10.7 Index]