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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Re-run TP53 module with correct flag #1526

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

In #1461, we re-ran the TP53 module with V22. However, as detailed in https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1515#issuecomment-1181699404 that run did not specify the flag OPENPBTA_TP53_FIGURES=1 which enforces that data in the data release, instead of from the collapse-rnaseq module, be used.

This PR fixes that oversight by running the module on V22 data with this flag. The most notable change is that polya AUC goes from 0.32 --> 0.38.

I have also added some information to the module README and the run script to document the different flags that can be used with the module.

sjspielman commented 2 years ago

This CI timed out, but the relevant module tp53_nf1_score completed CI successfully before time out, so we can merge.