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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Updated survival notebooks with LGG broad histology #1430

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

Closes #1416

This PR updates and re-runs the two survival notebooks (tp53 and immune) that consider an LGG grouping. The grouping should be the broad_histology, NOT the cancer_group. Results are broadly consistent.

jharenza commented 2 years ago

Just wanted to note, these would be rerun after v22 for the cancer group updates, if any, to non-LGG, is that your thinking @sjspielman ?

sjspielman commented 2 years ago

@jharenza I don't think I realized that might happen. I was under the impression that LGG v22 changes would involve changing cancer groups, but not broad histologies, for LGG.

If which samples are in this broad histology might change, then we should NOT merge this, and I'll convert this back to draft and block it with v22 to re-run later.

jharenza commented 2 years ago

I am hoping not, but upon QC of a new pull of the histologies file from our data warehouse, some path dx/free text have changed, and TBD whether this affects anything downstream. So probably safe to wait on this.

sjspielman commented 2 years ago

@jharenza This has now been re-run with V22. Some of the results have changed so please have a close look at those places where the notebook text has diffs.

sjspielman commented 2 years ago

I was wondering about the new Partial resection;Gross/Near total resection specimen! Will recode 👍

Will double check my text interpreting the table rows correctly!

sjspielman commented 2 years ago

@jharenza ready for another look!

sjspielman commented 2 years ago

This PR has previously passed CI, and changes have been smoothly run in a fresh RStudio session in Docker. Merging before checks complete.