Show a progress bar (TRUE or FALSE)? Might only work in Windows OS
minRT
Filter for measurements with retention time >= minRT. Otherwise set to FALSE.
maxRT
Filter for measurements with retention time <= maxRT. Otherwise set to FALSE.
minmz
Filter for measurements with m/z >= minmz. Otherwise set to FALSE.
maxmz
Filter for measurements with m/z <= maxmz. Otherwise set to FALSE.
ion_mode
"positive" or "negative" ionization. Otherwise set to FALSE, see details.
Details
The return value, a so-called MSlist object, is a simple R list object that contains (a) the raw measurement data, (b) intermediate/final
results of the peak picking procedure and (c) indices for random access, to be passed among functions.
Peaks are nested in EIC clusters which in turn are nested in partitions which in turn are subsets of measurements;
MSlist[[4]] is resorted accordingly during all peak picking steps.
Setting minRT, maxRT, minmz or maxmz allows you to filter your .mzML data.
On the one hand, this may be very useful if only being interested in certain ranges of an experiment.
On the other hand, this allows you to upload subset data of an experiment too large to be loaded into R at once.
ion_mode allows to filter scans of a specific polarity from .mzXML files, if not set to FALSE; useful for
files acquired under polarity switching.
Value
MSlist
State
MSlist[[1]]: tags the individual steps the MSlist has undergone.
Parameters
MSlist[[2]]: saves parameter settings.
Results
MSlist[[3]]: saves a result summary.
Scans
MSlist[[4]]: matrix with raw measurements (m/z, intensity, RT) and tags for partitions, EIC cluster and individual peaks.
Partition_Index
MSlist[[5]]: Index assigning partitions to sections in the raw measurment of MSlist[[4]]. Needed for fast (random) access during, e.g., plotting.
EIC_index
MSlist[[6]]: Index assigning EIC clusters to sections in the raw measurment of MSlist[[4]]. Required for fast access.
Peak_index
MSlist[[7]]: Index assigning picked peaks to sections in the raw measurment of MSlist[[4]]. Required for fast access.
Peaklist
MSlist[[8]]: Final peak list, cp. mzpick
Warning
Use plotMSlist to check your data in MSlist for consistency at an early stage before further processing.
Note
It is your responsibility to ensure your input files are centroided. If not, R may freeze and the peak picker will not return valid results.