Description Usage Arguments Value Author(s) See Also Examples
View source: R/do_findChromPeaks-functions.R
The function performs peak detection using the matchedFilter algorithm on chromatographic data (i.e. with only intensities and retention time).
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int |
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rt |
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fwhm |
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sigma |
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max |
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snthresh |
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... |
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()
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## Load the test file
data(faahko_sub)
## Update the path to the files for the local system
dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
## 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")
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