I am using R 3.2.0 and xcms 1.46.0 version for analysis of metabolomics dataset. I wish to know how can one save the xcmsSet data created in work space. I wish to use this xcmsSet data for running other software's.
Thanks,
Manohar
To save your whole workspace use save.image(). To save only the xcmsSet object use save or saveRDS.
Probably what you want though is a peak table. For that you use peakTable and save that table for example with write.csv.