PR 2 of 4 for SNV Consensus: Merge callers script

[cansavvy]

Purpose/implementation

This is a side analysis that originated from this original PR but after some reorganization has been split up and spread out.

This second PR merges the callers' VAF and TMB files for an output of four files. These four files can optionally be used in a later script to make plots and/or be used by a later script to make the final mutation consensus call.

The four output files:

• all_callers_vaf.rds - contains all the VAF file information for all callers.
• all_callers_tmb.rds - contains all the TMB file information for all callers.
• mutation_id_list.rds - a full list of the mutations that can be used for an UpSetR graph
• callers_per_mutation.rds - contains a breakdown for each mutation of what callers called it. Will be used to identify the consensus mutations.

Issue

For SNV caller comparison #161, #103 and Tumor Mutation Burden #3 and sort of #11

Directions for reviewers

I don't like having to use suppressWarnings to have it ignore combining columns. Is there a more seamless way to make this section less "shoot-in-the-foot" like?
Some of the writing steps are quite memory intensive and will undoubtedly add to the run time of the CircleCI tests. Do you have suggestions for decreasing the run time for this script?

Results

This script doesn't add results, but is a the next step toward getting the snv consensus.

Docker and continuous integration

These items were taken care of in #183

• 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.

PR Checklist

• Run a linter
• Set the seed- I didn't, but let me know if I should.
• Comments and/or documentation up to date
• Double check your paths
• Spell check any Rmd file or md file
• Restart R and run all notebooks fresh and save

[jaclyn-taroni]

What does this -w correspond to?

[cansavvy]

I used to have --overwrite have a short flag but then I deleted it. Forgot to delete it from the example.

[jaclyn-taroni]

A couple changes to documentation I would like to see before merging. This branch is difficult to test locally because it requires so much upstream stuff to have been run, so I have not pulled it locally and tested it out. It does seem reasonable though.