hpbenton / targeted_isotopes

Small script in R language to identify stable labeled isotopes in LC-MS data. Uses mzR and MSnBase

Quick Run

Parameters

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

Code to run

 out<-runSulphurFinder(atom="C", minScanTime=3, ppmDevN=20, snthresh=2, maxoFilt=1000, adductSelection=c("all", "standard") )
 

ToDO

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.

to be cleaned up later