findPeaks.matchedFilter,xcmsRaw-method {xcms} | R Documentation

## Peak detection in the chromatographic time domain

### Description

Find peaks in the chromatographic time domain of the profile matrix. For more details see `do_findChromPeaks_matchedFilter`.

### Usage

    ## S4 method for signature '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())

### Arguments

`object` | The `xcmsRaw` object on which peak detection should be performed.
`fwhm` | `numeric(1)` specifying the full width at half maximum of matched filtration gaussian model peak. Only used to calculate the actual sigma, see below.
`sigma` | `numeric(1)` specifying the standard deviation (width) of the matched filtration model peak.
`max` | `numeric(1)` representing the maximum number of peaks that are expected/will be identified per slice.
`snthresh` | `numeric(1)` defining the signal to noise cutoff to be used in the chromatographic peak detection step.
`step` | numeric(1) specifying the width of the bins/slices in m/z dimension.
`steps` | `numeric(1)` defining the number of bins to be merged before filtration (i.e. the number of neighboring bins that will be joined to the slice in which filtration and peak detection will be performed).
`mzdiff` | `numeric(1)` defining the minimum difference in m/z for peaks with overlapping retention times
`index` | `logical(1)` specifying whether indicies should be returned instead of values for m/z and retention times.
`sleep` | (DEPRECATED). The use of this parameter is highly discouraged, as it could cause problems in parallel processing mode.
`scanrange` | Numeric vector defining the range of scans to which the original `object` should be sub-setted before peak detection.

### Value

A matrix, each row representing an intentified chromatographic peak, with columns:

mz

  Intensity weighted mean of m/z values of the peak across scans.

mzmin

  Minimum m/z of the peak.

mzmax

  Maximum m/z of the peak.

rt

  Retention time of the peak's midpoint.

rtmin

  Minimum retention time of the peak.

rtmax

  Maximum retention time of the peak.

into

  Integrated (original) intensity of the peak.

intf

  Integrated intensity of the filtered peak.

maxo

  Maximum intensity of the peak.

maxf

  Maximum intensity of the filtered peak.

i

  Rank of peak in merged EIC (`<= max`).

sn

  Signal to noise ratio of the peak.

### Author(s)

Colin A. Smith

### References

Colin A. Smith, Elizabeth J. Want, Grace O'Maille, Ruben Abagyan and Gary Siuzdak. "XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification" Anal. Chem. 2006, 78:779-787. @family Old peak detection methods

### See Also

`matchedFilter` for the new user interface. `xcmsRaw`, `do_findChromPeaks_matchedFilter` for the core function performing the peak detection.

[Package xcms version 3.0.2 Index]