Some needed parameters are adductSelection="standard" minScanTime=3; ppmDevN=7.5; snthresh=2; maxoFilt=1000; plot.prog=F; atom<-"C"
You will also need a selection of compounds to target. This needs to have the following header names :
ID, name, mass, formula
out<-runSulphurFinder(atom="C", minScanTime=3, ppmDevN=20, snthresh=2, maxoFilt=1000, adductSelection=c("all", "standard") )
Currently the grouping code is not in a function Change code into objects Remove fixed quick run variables Have code to check number of cores on the machine.