Analysis update: Incorporate the feedback of HOPE non-HGG samples for v13

[zzgeng]

Purpose/implementation Section

What scientific question is your analysis addressing?

In HOPE cohort, some samples are not HGG and we got feedback from pathologist.
This PR is to incorporate the feedback to histologies file

What was your approach?

Incorporate the feedback of HOPE non-HGG samples for v13

What GitHub issue does your pull request address?

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

Which areas should receive a particularly close look?

analyses/molecular-subtyping-pathology/04-incorporate-pathology-feedback.Rmd

Is there anything that you want to discuss further?

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

This script should run with v13 data

Results

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

What is your summary of the results?

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.

[jharenza]

I made some updates to this - the sarcomas were not EWS, but rather a high grade sarcoma. The CNS BCOR is an embryonal tumor. I also went back and updated the HGG module to include the BRAF p.V640E alteration since we have that in v12. We can remove that snippet in v13.