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 1.12.1 Index]