V22 LGG subtyping (11/N)

jharenza commented 2 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

run v22 LGG subtyping

What was your approach?

What GitHub issue does your pull request address?

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

Reproducibility Checklist

[ ] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
[ ] This analysis has been added to continuous integration.

Documentation Checklist

[ ] This analysis module has a README and it is up to date.
[ ] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
[ ] The analytical code is documented and contains comments.

jharenza commented 2 years ago

Yes. I noticed this yesterday and filed https://github.com/PediatricOpenTargets/ticket-tracker/issues/338

I see two options - I can manually update these at the base file level or wait until the data warehouse is updated and do a new pull of the file, but the latter will take longer, so I will probably do the former. I don't think this would affect any other modules based on the diagnoses with issues, but would you want me to rerun all modules?

jaclyn-taroni commented 2 years ago

I don't think we need to rerun additional modules.

If we don't need to join on pathology_free_text_diagnosis (and maybe we make that decision based on if that impacts any results), removing that seems like it would have the benefit of being a quick change that is tracked in the code base.

jharenza commented 2 years ago

I did update the code locally to test not to join on it, but unfortunately, we do need it for glialneuronal subtyping, which occurs within this module. Will try to update this later tonight.

AlexsLemonade / OpenPBTA-analysis