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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Re-run notebooks in `tp53_nf1_score` module #1242

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

As discussed, the tp53_altered_status.tsv file created in the tp53_nf1_score module has some slight numerical inconsistencies when re-run. It is likely that these minor discrepancies were caused by initially running the notebook producing this data file outside of Docker, because running within Docker is consistent.

As none of the notebooks in this module contained a sessionInfo(), this PR has re-run all notebooks in this module to include that information. Along with this, the TSV file is updated with the Docker-run version, and some of the PDFs were updated with current aspect ratios (they may have also been out of sync).

sjspielman commented 2 years ago

I don't know that I expect all the quotes around NA values in that file Oh, I hadn't noticed that, interesting. As long as they are still NA's!