Update ATRT molecular subtyping module to use GSVA scores

[jaclyn-taroni]

Purpose/implementation Section

With #386, we have updated single-sample gene set enrichment scores. Specifically, we have GSVA scores that follow a Gaussian distribution. Here I am updating the molecular-subtyping-ATRT module to use these new scores.

I have made the following changes:

• Updated the subsetting files (00-subset-files-for-ATRT.R) and main data wrangling (01-ATRT-molecular-subtyping-data-prep.Rmd) steps of this module to use the GSVA scores
• Updated the module documentation in both molecular-subtying-ATRT README and the analyses README
• Updated analyses/ssgsea-hallmark/README.md to

What GitHub issue does your pull request address?

Related to #244

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

Is there anything else that needs to be updated that I have missed? I have covered everything that I wrote in #368 (comment)

Results

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

Updates analyses/molecular-subtyping-ATRT/results/ATRT_molecular_subtypes.tsv -- we will need someone with domain expertise to review this table and see what, if any, tweaks need to be made.

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

[cansavvy]

Cool. LGTM!! Just one minorly minor request that you can take or leave. I notice that most of the data.frames being read and manipulated here are printed out so the reader can see what they look like. Following this pattern, you also print out a preview of the GSVA data? It would help readers follow along with what is happening, but also it seems strange that it is the only dataset that is not being printed out with %>% head(n =15).

[jaclyn-taroni]

Good point! I'll make that change!