peaksWithMatchedFilter: Identify peaks in chromatographic data using matchedFilter

In sneumann/xcms: LC-MS and GC-MS Data Analysis

Identify peaks in chromatographic data using matchedFilter

Description

The function performs peak detection using the matchedFilter algorithm on chromatographic data (i.e. with only intensities and retention time).

Usage

peaksWithMatchedFilter(
  int,
  rt,
  fwhm = 30,
  sigma = fwhm/2.3548,
  max = 20,
  snthresh = 10,
  ...
)

Arguments

int	numeric with intensity values.
rt	numeric with the retention time for the intensities. Length has to be equal to length(int).
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) with the maximal number of peaks that are expected/ will bbe detected in the data
snthresh	numeric(1) defining the signal to noise cut-off to be used in the peak detection step.
...	currently ignored.

Value

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

• "rt": retention time of the peak's midpoint (time of the maximum signal).

• "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 (original) intensity of the peak.

• "maxf"" maximum intensity of the filtered peak.

• "sn": signal to noise ratio of the peak.

Author(s)

Johannes Rainer

See Also

matchedFilter for a detailed description of the peak detection method.

Other peak detection functions for chromatographic data: peaksWithCentWave()

Examples

## Load the test file
faahko_sub <- loadXcmsData("faahko_sub")

## Subset to one file and drop identified chromatographic peaks
data <- dropChromPeaks(filterFile(faahko_sub, 1))

## Extract chromatographic data for a small m/z range
chr <- chromatogram(data, mz = c(272.1, 272.3), rt = c(3000, 3200))[1, 1]

pks <- peaksWithMatchedFilter(intensity(chr), rtime(chr))
pks

## Plotting the data
plot(rtime(chr), intensity(chr), type = "h")
rect(xleft = pks[, "rtmin"], xright = pks[, "rtmax"], ybottom = c(0, 0),
    ytop = pks[, "maxo"], border = "red")

sneumann/xcms documentation built on Nov. 23, 2024, 6:53 p.m.