This is a convenience function that performs an end to end analysis of an Sciex MRM run; it can be used when the intermediate data structures (total ion chromatograms, shot lists, .wiff file readers) are not required.
processAllMRMAreas(wiffFile, wiffScanFile, removeBaseline = TRUE, ...)A list containing two data frames: ejections, with all extracted
TIC peaks for all runs, as output by measureEjections(), and massAreas,
containing the measured areas for all mass transitoins and all peaks in all
runs, as output by getMRMAreas(). Both data frames contain an addtional
wiffSample column indicating which run within the file the values were
extracted from.
A valid file path to the Sciex data file (extension .wiff) containing the metadata for one or more EchoMS runs
An valid file path the the Sciex scan file (extension .wiff.scan) containing the full raw EchoMS data
If TRUE, baseline intensity for each mass transition will be subtracted from the intensities in each ejection, to account for baseline intensities measured near the lower limit of quantitation
Additional optional parameters to be passed to measureEjections()