Revision: Recalculate and assess quanTIseq scores at threshold

[sjspielman]

To assess the affects of tumor purity on our results, we should recalculate quanTIseq predicted celltype fractions, survival models, considering only samples that have tumor_fraction>= median tumor fraction (https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1622).

Specifically, we should run the following models and compare results to original results with all tumors:

• monocytes dominant in Schwannomas and neurofibromas
  • https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/b0fdf6f24fe9c021f22e8b7da348708f68877ee5/content/03.results.md?plain=1#L277-L278
• CD8+ T-cell infiltration across all cancer groups was low, except MB3/4 and "outlier tumors"
  • https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/b0fdf6f24fe9c021f22e8b7da348708f68877ee5/content/03.results.md?plain=1#L282
• surprisingly, classically-cold tumors have higher immune fractions, which we interpreted as a consequence of the method itself. We'll want to reconsider that interpretation if the thresholdified analysis shows a different trend.
  • https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/b0fdf6f24fe9c021f22e8b7da348708f68877ee5/content/03.results.md?plain=1#L283
• hot/cold phenotype results
  • https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/b0fdf6f24fe9c021f22e8b7da348708f68877ee5/content/03.results.md?plain=1#L292