findPeaks-methods {xcms}R Documentation

Feature detection in the chromatographic time domain

Description

Arguments

object xcmsSet object
fwhm full width at half maximum of matched filtration gaussian model peak
sigma standard deviation of matched filtration model peak
max maximum number of peaks per extracted ion chromatogram
snthresh signal to noise ratio cutoff
step step size to use for profile generation
steps number of steps to merge prior to filtration
mzdiff minimum difference in m/z for peaks with overlapping retention times
index return indicies instead of values for m/z and retention times
sleep number of seconds to pause between plotting peak finding cycles

Value

A matrix with columns:

i rank of peak identified in merged EIC (<= max)
mz weighted (by intensity) mean of peak m/z across scans
mzmin m/z of minimum step
mzmax m/z of maximum step
ret retention time of peak midpoint
retmin leading edge of peak retention time
retmax trailing edge of peak retention time
into integrated area of original (raw) peak
intf integrated area of filtered peak
maxo maximum intensity of original (raw) peak
maxf maximum intensity of filtered peak

Methods

object = "xcmsRaw"
findPeaks(object, fwhm = 30, sigma = fwhm/2.3548, max = 5, snthresh = 10, step = 0.1, steps = 2, mzdiff = 0.8 - step*steps, index = FALSE, sleep = 0)

See Also

xcmsRaw-class


[Package xcms version 1.2.0 Index]