chromatogram method extracts chromatogram(s) from an
Depending on the provided parameters this can be a total ion chromatogram
(TIC), a base peak chromatogram (BPC) or an extracted ion chromatogram
(XIC) extracted from each sample/file.
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Parallelisation backend to be used, which will
depend on the architecture. Default is
mz allow to specify the MS
data slice from which the chromatogram should be extracted.
aggregationSum allows to specify the function to be
used to aggregate the intensities across the mz range for the same
retention time. Setting
aggregationFun = "sum" would e.g. allow
to calculate the total ion chromatogram (TIC),
aggregationFun = "max" the base peak chromatogram (BPC).
The length of the extracted
i.e. the number of available data points, corresponds to the number of
scans/spectra measured in the specified retention time range. If in a
specific scan (for a give retention time) no signal was measured in the
specified mz range, a
NA_real_ is reported as intensity for the
retention time (see Notes for more information). This can be changed
By default or if
rt are numeric vectors, the
function extracts one
Chromatogram object for each file
object. Providing a numeric matrix with argument
enables to extract multiple chromatograms per file, one for each row in
the matrix. If the number of columns of
rt are not
equal to 2,
range is called on each row of the matrix.
chromatogram returns a
MChromatograms object with
the number of columns corresponding to the number of files in
object and number of rows the number of specified ranges (i.e.
number of rows of matrices provided with arguments
rt). The 'featureData' of the returned object contains columns
"mzmax" with the values from input argument
mz (if used) and
"rtmax" if the input
rt was used.
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## Read a test data file. library(msdata) f <- c(system.file("microtofq/MM14.mzML", package = "msdata"), system.file("microtofq/MM8.mzML", package = "msdata")) ## Read the data as an MSnExp msd <- readMSData(f, msLevel = 1) ## Extract the total ion chromatogram for each file: tic <- chromatogram(msd) tic ## Extract the TIC for the second file: tic[1, 2] ## Plot the TIC for the first file plot(rtime(tic[1, 1]), intensity(tic[1, 1]), type = "l", xlab = "rtime", ylab = "intensity", main = "TIC") ## Extract chromatograms for a MS data slices defined by retention time ## and mz ranges. rtr <- rbind(c(10, 60), c(280, 300)) mzr <- rbind(c(140, 160), c(300, 320)) chrs <- chromatogram(msd, rt = rtr, mz = mzr) ## Each row of the returned MChromatograms object corresponds to one mz-rt ## range. The Chromatogram for the first range in the first file is empty, ## because the retention time range is outside of the file's rt range: chrs[1, 1] ## The mz and/or rt ranges used are provided as featureData of the object fData(chrs) ## The mz method can be used to extract the m/z ranges directly mz(chrs) ## Also the Chromatogram for the second range in the second file is empty chrs[2, 2] ## Get the extracted chromatogram for the first range in the second file chr <- chrs[1, 2] chr plot(rtime(chr), intensity(chr), xlab = "rtime", ylab = "intensity")
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