Updates to chromosomal-instability

[cansavvy]

Purpose/implementation Section

What scientific question is your analysis addressing?

The items on #487 :

• CNV consensus seg file needs to be used.
• The excluded regions BED file needs to be used
  - For the denominator for calculating densities
  - For marking NA on heatmap
• Flexibility parameters need to be added for calling breakpoints as the same between SV and CNV data. See this comment

What was your approach?

• Excluded regions BED:
  Regions are considered NA based on the percentage of the bin that is covered by an cnv_excluded_regions.bed. The percent cutoff for each bin can be set by perc_cutoff argument for break_density function calculation.

• Flexibility parameters:
  CNV and SV data are now combined by an intersection the flexibility of which is controlled by --gap 5 parameter. This gap parameter is passed directly to GenomicRanges' mergeByOverlaps function's maxgap parameter. E.g. for a gap parameter of 5, a CNV or SV breakpoint within 5 bp of each other for the same sample will be considered the same.

• Somewhat related but not really, I also added a drop-sex argument to the 00-setup script.

What GitHub issue does your pull request address?

#487

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

Which areas should receive a particularly close look?

• The break density function is where the percent overlap is calculated. Can someone make sure that is representing what I think it's representing?
• 00-setup-breakpoint-data.R's changes for the intersection between CNV and SV also should have a careful look.
• Are the added options: --gap, perc_overlap and --drop-sex clear and seem like the logic that surrounds them is sensible?

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

Yes. Let me know what changes you suggest for the plots.

Results

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

The plots are updated to be like this:

What is your summary of the results?

Here's the rendered html: https://cansavvy.github.io/openpbta-notebook-concept/chromosomal-instability/01-plot-chromosomal-instability.nb.html

Reproducibility Checklist

These items were done previously.

• 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.

[jashapiro]

A few comments on what I have seen so far, but I am getting confused about where the NA data is introduced and such, which hopefully you can clarify.

[jashapiro]

Will this catch adjacent breaks, like a break at position 10 and another at 11? Because those should really be the same, but I can't tell if they are considered gap of 0 or 1.

[cansavvy]

From GenomicRanges docs: The gap between 2 ranges is the number of positions that separate them. The gap between 2 adjacent ranges is 0. I interpret this to mean that maxgap = 0, means they are right next to each other. Is this what we want?

[jashapiro]

Do we want to exclude the small regions if we are going to calculate overlaps using them later?

[cansavvy]

We can keep them.

[jashapiro]

I don't know why these ticks aren't showing up in the rendered image?

[cansavvy]

Per our in person discussion, @jashapiro , I will work on splitting this up into more manageable PRs and perhaps in a reorganized set of notebooks. Stay tuned. 📺

[cansavvy]

After doing reorganizing of these changes, I'm going to break up this into multiple PRs. Closing this original PR now.