peaksWithMatchedFilter {xcms} | R Documentation |
The function performs peak detection using the matchedFilter algorithm on chromatographic data (i.e. with only intensities and retention time).
peaksWithMatchedFilter(int, rt, fwhm = 30, sigma = fwhm/2.3548, max = 20, snthresh = 10, ...)
int |
|
rt |
|
fwhm |
|
sigma |
|
max |
|
snthresh |
|
... |
currently ignored. |
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.
Johannes Rainer
matchedFilter for a detailed description of the peak detection method.
Other peak detection functions for chromatographic data: peaksWithCentWave
## Read one file from the faahKO package od <- readMSData(system.file("cdf/KO/ko15.CDF", package = "faahKO"), mode = "onDisk") ## Extract chromatographic data for a small m/z range chr <- chromatogram(od, mz = c(272.1, 272.3))[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")