V22 molecular subtyping integrate (13/N) - Githubissues

AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project

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V22 molecular subtyping integrate (13/N) #1446

Closed jharenza closed 2 years ago

jharenza commented 2 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

Run molecular subtype integrate to get final histologies file for v22.

What was your approach?

Run

echo "Run integrate subtyping"
bash ../analyses/molecular-subtyping-integrate/run-subtyping-integrate.sh

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

The diff for pbta-histologies.tsv is not super helpful for spot checking things unfortunately 😢

Regarding this - maybe I can run some of the summary table modules using this new file/staggered on top of this PR, specifically Table 1, S1, and rerun https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/sample-distribution-analysis?

🤞 that since everything along the way checks out, this file should also, but I can run the above to see how the new results differ.