Vignette or example for running as a non-interactive script?

[cgpu]

Awesome work!

I would like to give it a try as a non-interactive R script, ideally to be able to combine with
https://github.com/francescodc87/IPA in a workflow at some point.

Could you point me to an example script or guidelines on how to go about for running the analysis in cli without having to interact with the shinny app?

Thanks again!
Christina :)

[joannawolthuis]

Hi Christina, thank you! :D Your code looks really interesting, are you thinking more on the database side of things? You may want to check out MetaDBparse, although I've been a bit behind on writing a proper vignette I can do so if you let me know which parts you are most interested in :)

[cgpu]

Hi @joannawolthuis ! Thanks once again for the prompt response! I'm mostly interested in annotation of MS data. No MS/MS unfortunately, so I will have to try level 2-3 annotation with xcms and CAMERA output for MS1.

My current intention is to check with the following 3 tools:

• https://github.com/francescodc87/IPA (check their paper, it's actually very interesting)

• https://github.com/osenan/cliqueMS

• {MetaboShiny} 📦 backend if possible!

What functions from MetaDBparse can I use for attempting to annotate my "metabolic features"
if the only available data I have are: adducts and isotopes (from CAMERA) and intensity matrix fromxcms ?

Thanks in advance for the help, much appreciated!

[joannawolthuis]

Sorry for the terribly slow answer, I thought I already had answered you but I was mistaken D:! Can you show me an example if your data, perhaps? The searchDB function in MetaDBparse takes M/Z values, then you can filter specific isotopes and/or adducts from those results if you like. I still need to write a proper documentation for that package, but I can help you with running your data through it if you have a (dummy) example of what your input would be.