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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_nf1_score module with v22 #1461

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

This PR re-runs the tp53_nf1_score analysis module with V22. The primary diffs are in the LGAT files, which makes sense for what we expect to see changing here.

sjspielman commented 2 years ago

I think that at least one plot tp53_cancer_group.pdf will depend on the updates/decisions in https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1401.

I'm not sure this is strictly necessary for a figure like this which won't be going into the manuscript? There's a ton of "deprecated" figures using different groupings sprinkled across many analysis modules which we hadn't been updating so strictly. The TP53 figures for the manuscript (which definitely need the right cancer groupings!) are made in figures/scripts/fig4-tp53-telomerase-panels.R, and we'll be doing a separate re-run of that script after #1401 goes in.

All that said, can't hurt to just wait a bit for #1401 and re-run again! Edit - given that it looks like we'll have some pretty salient changes, definitely need to run again.

sjspielman commented 2 years ago

I've re-run this again now that #1401 has been merged. All .tsv diffs are just minor numerical tolerance differences, and overall results remain stable. I also updated the PDFs pointed out in https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1461#pullrequestreview-1017131762 to use the correct palettes.