xcms (version 1.48.0)

findPeaks.MSW-methods: 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

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)

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.

See Also

findPeaks-methods xcmsRaw-class peakDetectionCWT