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taxonomicallyinformedannotation / tima-r

https://taxonomicallyinformedannotation.github.io/tima-r/
https://taxonomicallyinformedannotation.github.io/tima-r
GNU General Public License v3.0
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FinalResults table not mantaining library, molecular formula and smiles information #22

Closed DanielCR92 closed 2 years ago

DanielCR92 commented 2 years ago

I performed feature annotation using ISDB (spec_lib_matcher) and noticed that after using TIMA (annotate: FALSE for MS1 annotations on the process_annotations.yaml), in some annotated features the information in the library, molecular formula and smiles column is lost, even though the annotation coming from ISDB and containing that information is used.

I followed back to the pretreated, filled, and treated annotation files and they contained their respective information, so i think this information is lost in the last step of the process, after running source(file = "inst/scripts/process_annotations.R").

I attach the original ISDB file and the TIMA final results file. ISDB_annotations.zip FinalResults.zip

Adafede commented 2 years ago

Hi @DanielCR92, thank you for your issue.

It looks like an interesting bug, sadly, I am not able to reproduce your error. Could you also attach your config files?

Thanks

Adafede commented 2 years ago

@DanielCR92 I tried a fix with 8614b1b9259e03718e666d7f119c87b60c427302, could you try pulling everything again, rebuilding the package, and tell me if solved?

DanielCR92 commented 2 years ago

Hello @Adafede! I attach the config files. config.zip

For this particular job I ran all the commands on the first vignette of the documentation (library preparation), then I ran source(file = "inst/scripts/prepare_isdb.R"), source(file = "inst/scripts/prepare_edges.R"), source(file = "inst/scripts/prepare_features_components.R") and source(file = "inst/scripts/prepare_features_classification.R"); and finally source(file = "inst/scripts/process_annotations.R").

I also noticed the bug present on the final results table when running the initial example (Rscript inst/scripts/tima.R)

I'm gonna check the fix. Thank you very much!

DanielCR92 commented 2 years ago

Ran everything again and it worked perfectly, all the information is now mantained.

Thanks!

Adafede commented 2 years ago

Thank you for pointing it out at the beginning! I'll close :)