add PXA to molecular subtype

[zzgeng]

Purpose/implementation Section

What scientific question is your analysis addressing?

Add pleomorphic xanthoastrocytoma (PXA) to HGG molecular subtyping module

What was your approach?

Based on WHO guidebook, samples with

• BRAF mutation and
• homozygous deletion of CDKN2A and/or CDKN2B and
• methylation profile as PXA
  as "PXA"

What GitHub issue does your pull request address?

#443

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

Which areas should receive a particularly close look?

03, 07 R script and output results.

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?

Yes

Results

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

Table

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.

[rjcorb]

The added code for PXA subtyping aligns with the overall workflow for HGG subtyping, so I am approving. My only comment is this code create a PXA subtype data frame to be added to final subtyping df, despite there not currently being any samples subtyped as PXA. But for oligodendroglioma, there is just a check for any samples with this subtype, and since there are currently zero there is no code to create a df and add to final subtyped df. It may be worth using the same strategy for oligo as is done for PXA: no samples currently, but will be added to final output in the future if any oligo samples are added to future cohort.

[jharenza]

@zzgeng can you fix conflicts here/merge dev/rerun