Modification of survival analysis WIP PR

Purpose/implementation Section

What scientific question is your analysis addressing?

This

What was your approach?

1) Make the quantile calculation into a function so that we can use matching quantiles 2) Adding a for loop to iterate through all 3 data frames with their individual quantiles 3) Add 2 more functions for generating the statistics for paper writing

What GitHub issue does your pull request address?

https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1210

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

1) Note that since I cannot push to upstream surv branch - this PR is against the surv branch 2) Also, I think the additional changes we see is due to the fact that the current surv is not up to date with the master - should go away when upstream surv is in sync.

Is there anything that you want to discuss further?

Please let me know if you want me to start a PR against the master instead etc.

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes.

Results

What types of results are included (e.g., table, figure)?

Tables and figures - the modifications of the code generated the same results as original PR. It is just a code change that loop all 3 dfs and their percentiles into the survival model.

What is your summary of the results?

N/A - see original PR.

Reproducibility Checklist

[ ] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
[ ] This analysis has been added to continuous integration.

Documentation Checklist

[ ] This analysis module has a README and it is up to date.
[ ] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
[ ] The analytical code is documented and contains comments.

AlexsLemonade / OpenPBTA-analysis