Add Interaction sample calculation notebook

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

The notebook added here records:

• Total N of PBTA samples included in co-occurrence analysis
• Number of significant events (co-occurrence/mutual exclusivity)
• Number of HGG-specific significant events
• Ratio of hgg/total significant events

What was your approach?

Calculate the above from cooccur_top50.ALL.tsv and cooccur_top50.Diffuse-astrocytic-and-oligodendroglial-tumor.tsv

What GitHub issue does your pull request address?

This PR closes #1391

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

Which areas should receive a particularly close look?

NA

Is there anything that you want to discuss further?

No

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)?

notebook with results

What is your summary of the results?

These numbers match those in the manuscript

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.

[jharenza]

Yeah good point, will do. I was a little unsure how to add this since the dir structure is a bit different

[jharenza]

Yes, didn't see that one, thanks!

[jharenza]

@sjspielman ready for re-review. This was a very early module and so the readme doesn't explicity list every script and file as do others, so if we want to update, maybe @jashapiro can update that part. I updated more generally. In addition, I used a bash run script to be consistent with every other module.