Updated analysis: survival analysis generalization

[runjin326]

What analysis module should be updated and why?

survival analysis that is currently in PR 1208

What changes need to be made? Please provide enough detail for another participant to make the update.

1) Currently the script has non-HGAT and PBTA all commented out - need to add back as a loop function to run the analyses on all data frames 2) When looping across different data frames, the quantiles used for HGAT/PBTA and non-HGAT need to be taken into control 3) Add this function as well for output for table:

pairwise_survdiff(formula = Surv(OS_days, OS_status) ~ pheno_0.5, 
                  data = meta_no_hgat, 
                  p.adjust.method = "BH", rho = 0)

What input data should be used? Which data were used in the version being updated?

pbta-histologies.tsv
independent-specimens.rnaseq.primary-plus-stranded.tsv
tp53_altered_status.tsv
TelomeraseScores_PTBAStranded_FPKM.txt

When do you expect the revised analysis will be completed?

1-2 days.

Who will complete the updated analysis?

@runjin326

[jaclyn-taroni]

I'm going to close this in favor of what's outlined in https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1208#issuecomment-996356663