search

ElucidataInc / ElMaven

LC-MS data processing tool for large-scale metabolomics experiments.
https://resources.elucidata.io/elmaven/
GNU General Public License v2.0
88 stars 52 forks source link

Make CLI and GUI behavior consistent #403

Open shubhra-agrawal opened 7 years ago

shubhra-agrawal commented 7 years ago

This came up while looking at #356.

reduceGroups function in CLI removes groups that have a high overlap in terms of rt and m/z. Code for the same functionality is present in addPeakGroup in PeakDetector (used in GUI) but changes have been made such that it is never used.

Removing duplicate groups makes sense for automated or untargeted search; but not so much for targeted search because: 1) getting the same group annotated as two compounds is not a problem 2) m/z overlap is calculated using ppmMerge (mass domain resolution) parameter set from Automated Search

chubukov commented 4 years ago

I'm not sure if there is still a plan to take this up, but I figured I'd note here that I've been using -p 0 on the command line, which seems like it should result in no merging being done. It would be nice to have this more explicit.