findPeaks.matchedFilter-xcmsRaw-method: Peak detection in the chromatographic time domain

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

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.

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.