Issue 1248

[sjspielman]

Purpose/implementation Section

This PR updates the mutational-signatures module to explore the relationship among TP53 status, hypermutators, and signature exposure

What GitHub issue does your pull request address?

Issue #1248

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

Which areas should receive a particularly close look?

Results are now integrated to simultaneously explore signatures 3, 18, and MMR2. There are no strong trends here, but there are some interesting observations for the individual samples that are described in the notebook.

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 exploratory figures in the notebook. At this time nothing is exported.

Reproducibility Checklist

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

Documentation Checklist

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

[sjspielman]

Note the forced push above is because github problems meant the last commit wasn't being sent to CI. Now it's running.

[jharenza]

Updates on the above two for TMZ treatment timelines (looks like tx was after surgery in both cases):

7316-2307 - treatment of tem was started 88 days after their biopsy.
7316-2640 - no chemo start and stop dates were recorded but it's noted that radiation started 35 days after surgery. (and from Cassie Kline: "can be concomitant depending - but RT always at beginning of therapy regardless.")