View source: R/functions-XCMSnExp.R
findChromPeaksIsolationWindow function allows to perform a
chromatographic peak detection in MS level > 1 spectra of certain isolation
windows (e.g. SWATH pockets). The function performs a peak detection,
separately for all spectra belonging to the same isolation window and adds
them to the
chromPeaks() matrix of the result object, information about
the isolation window they were detected in is added to
Note that peak detection with this method does not remove previously
identified chromatographic peaks (e.g. on MS1 level using the
findChromPeaks() function but adds newly identified peaks to the existing
Isolation windows can be defined with the
isolationWindow parameter, that
by default uses the definition of
chromatographic peak detection is performed for all spectra with the same
isolation window target m/z (seprarately for each file). The parameter
param allows to define and configure the peak detection algorithm (see
findChromPeaks() for more information).
findChromPeaksIsolationWindow( object, param, msLevel = 2L, isolationWindow = isolationWindowTargetMz(object), ... )
Peak detection parameter object, such as a
CentWaveParam object defining and configuring the chromographic
peak detection algorithm.
currently not used.
XCMSnExp object with the chromatographic peaks identified in spectra of
each isolation window from each file added to the
Isolation window definition for each identified peak are stored as additional
Johannes Rainer, Michael Witting
reconstructChromPeakSpectra() for the function to reconstruct
MS2 spectra for each MS1 chromatographic peak.
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