Chromosomal Instability (PR 2 of 3): The functions

[cansavvy]

Purpose/implementation Section

This second PR has the functions that will be used for calculating and plotting chromosomal breakpoints.

What scientific question is your analysis addressing?

This was the task:

Generating a measure of chromosomal instability (CIN) burden that can be plotted by tumor type

I borrowed concepts from https://github.com/gonzolgarcia/svcnvplus for generating breakpoint density. I calculate breakpoint density and in a later PR, I will plot this data by tumor type.

What was your approach?

These functions calculate breakpoint density for CNV, SV and combined CNV and SV and them plot them. I have an example of the output plot below.

What GitHub issue does your pull request address?

The first part of #394 (the recurrently altered genes part will be a different PR series that will undoubtedly use the functions this PR series uses as well as maybe additional ones).

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

I have ideas about how to make these functions more generalizable, but before I get too far into the weeds, I need another pair of eyes to let me know how they look so far.

• Are there places I can make these functions more..
  - ...Efficient?
  - ...DRYer?
  - ...Easier to use?
  - ...Better documented?

Keep in mind, I realize the comments and suggestions about these functions make change as you see them being used in context in the subsequent PRs. Don't worry about them being perfect in context at this stage, I'm more looking for places where my approach should be changed or optimized in general.

Results

No results yet, that will be the next PR, just the functions. Here's an example plot of what these functions create:

Reproducibility Checklist

This will be added to circleCI in the third PR. There are no new packages that need to be added to the Dockerfile so that is set.

• 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.
• This analysis is recorded in the table in analyses/README.md.

[jaclyn-taroni]

I found a few typos and it looks like all of @sjspielman's comments have been addressed for the moment. I am going to approve in the interest of making #419 a bit more manageable, but we can revisit these files if something comes up during that review. I will commit my suggested changes.