findPeaks.matchedFilter-methods {xcms}R Documentation

Feature detection in the chromatographic time domain

Description

Find peaks in extracted the chromatographic time domain of the profile matrix.

Arguments

object xcmsRaw 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:

mz weighted (by intensity) mean of peak m/z across scans
mzmin m/z of minimum step
mzmax m/z of maximum step
rt retention time of peak midpoint
rtmin leading edge of peak retention time
rtmax 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
i rank of peak identified in merged EIC (<= max)
sn signal to noise ratio of the peak

Methods

object = "xcmsRaw"
findPeaks.matchedFilter(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)

Author(s)

Colin A. Smith, csmith@scripps.edu

See Also

findPeaks-methods xcmsRaw-class


[Package xcms version 1.14.1 Index]