Update ATRT subtyping to use minimal set of genes

[jaclyn-taroni]

Purpose/implementation Section

What scientific question is your analysis addressing?

Molecular subtyping of ATRT tumors

What was your approach?

I updated the notebook that generates the final table to use the minimal gene set mentioned here: #244 (comment)

What GitHub issue does your pull request address?

#244

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

View the rendered notebook here: https://jaclyn-taroni.github.io/openpbta-notebook-concept/01-ATRT-molecular-subtyping-data-prep.nb.html

And the table here: https://github.com/jaclyn-taroni/OpenPBTA-analysis/blob/0a452f103324c4f09ab38d039f80d66f494f66b0/analyses/molecular-subtyping-ATRT/results/ATRT_molecular_subtypes.tsv

Reproducibility Checklist

• 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.

[cbethell]

LGTM 👍

[jharenza]

This looks good to merge to me!

[jaclyn-taroni]

Because we had some issues where the SMARCB1 losses were not showing up (#473), I reran this using the new consensus files (from focal-cn-file-preparation and #453 (comment)). We still find losses:

table(old_table$SMARCB1_focal_status, new_table$SMARCB1_focal_status)
         
          loss neutral
  loss      20       3
  neutral    0       3

(where old_table is pre-dbc6818). So we have a few losses that are now neutral when we use the consensus file and a few more samples where the SMARCB1 values are missing - this can happen where we have missing copy.num values in the consensus SEG file (see: https://alexslemonade.github.io/OpenPBTA-analysis/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html#add_ploidy_and_status).

[jaclyn-taroni]

The most recent non-documentation change (dbc6818) passed, so I'm going to merge this before Circle finishes.