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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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V22 subtyping (1/N) #1433

Closed jharenza closed 2 years ago

jharenza commented 2 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

I am going to stagger these so the changes aren't so overwhelming. For this PR, I am running only GSVA (no changes) and then TP53:

https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/e99c13550956c95fa83e9c811515e04a01a8c3d4/scripts/run-for-subtyping.sh#L12-L16

What was your approach?

Ran the lines above, but had some errors in the TP53 module which required some code changes:

  1. Remove https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/e99c13550956c95fa83e9c811515e04a01a8c3d4/analyses/tp53_nf1_score/run_classifier.sh#L90-L92 and add this to the data release. This script was using pbta-histologies.tsv, and we really don't need to rerun if we keep the file from the previous step of generate data analysis files. See new PR to maintain this file #1432. It is also now included in #1365
  2. Update focal-cn-file-preparation/02-add-ploidy-consensus.Rmd to pull the above seg status file from /data
  3. Add code around https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/e99c13550956c95fa83e9c811515e04a01a8c3d4/analyses/tp53_nf1_score/run_classifier.sh#L114-L118 to skip these steps for subtyping, since the plots require fields created post-subtyping

What GitHub issue does your pull request address?

1426 - partial

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

Which areas should receive a particularly close look?

code updates

Is there anything that you want to discuss further?

No, everything now runs as expected. File changes are minor.

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

yes

Results

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

TP53 module file changes

What is your summary of the results?

as expected

Reproducibility Checklist

Documentation Checklist