xcms (version 1.48.0)

findPeaks.matchedFilter-methods: 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. Only used to calculate the actual sigma, see below.

sigma

standard deviation (width) 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

scanrange

scan range to process

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, scanrange= numeric())

See Also

findPeaks-methods xcmsRaw-class