Extract the peak areas for MRM mass transitions for a given well
getMRMAreas(scanfile, tic, sample, ejections, well, removeBaseline = TRUE)A data frame containing the total intensity for each mass transition and each ejection; see Details for column specifics.
A file path to a Sciex raw scan file (extension .wiff.scan) containing the raw data referenced by the .wiff file from which the other parameters were extracted
A total ion chromatogram data.frame as extracted by getTIC() or
getAllTIC()
A "sample" object representing a run in a .wiff file, from the
samples field of an rtmsWiffReader object, containing information about
the mass transitions measured in that run
An ejection table listing the timing and boundaries of the
total ion chromatogram peaks for all shots in the run, as returned by
measureEjections()
The well (a string) or well index (an integer) to be measured
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
The table return includes a measurement of total area for each of the mass
transitions listed in sample. It contains one row for each measured shot
each mass transition, with the following columns:
shotorder: The order of the peak within the shots fired during the run
well: The alphanumeric well name of the well from which the shot was
fired
time: The time (in seconds) after the beginning of the run at which the
intensity from the shot was at its peak
massindex: The index of the measured mass transition in the set of masses
in the given sample
mass: The name of the mass transition measured (often a compound name or
id)
area: The intensity area (in counts) for that particular mass transition
from that shot's peak