findPeaks.MSW-methods: Feature detection for single-spectrum non-chromatography MS...

In sneumann/xcms-presvnbridge: LC/MS and GC/MS Data Analysis

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	m/z value of the peak at the centroid position
mzmin	m/z value at the start-point of the peak
mzmax	m/z value at the end-point of the peak
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
intf	always NA
maxf	maximum MSW-filter response of the peak
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, Joachim kutzera, sneumann|[e-mail]

See Also

findPeaks-methods xcmsRaw-class peakDetectionCWT

sneumann/xcms-presvnbridge documentation built on May 30, 2019, 6:02 a.m.