New Analysis: add Pineoblastoma subtype module

[zzgeng]

Purpose/implementation Section

What scientific question is your analysis addressing?

add Pineoblastoma subtype module

What was your approach?

add Pineoblastoma subtype module using methylation subclass

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-PB/

Is there anything that you want to discuss further?

need to update molecular-subtype-pathology and molecular-subtype-integreate

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

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]

hi @zzgeng - I made some minor updates to the subtype names, and updated the readme. I also removed PNET since it was pulling PNET in the absence of path free text being a pineoblastoma and we want to subtype those in embryonal separately. I also updated pathology and integrate modules and ran those. Can you do a once over and check this, AND create a flow diagram for this? Then, we can get it merged?

[jharenza]

Quick question- maybe I missed it- in your flow, O think we might want path dx == pineoblastoma OR free text contains any of those ? That way PNET would come in only if we had a free text pineoblastoma..

[zzgeng]

Quick question- maybe I missed it- in your flow, O think we might want path dx == pineoblastoma OR free text contains any of those ? That way PNET would come in only if we had a free text pineoblastoma..

When I got path dx and free text for this module, I took a look at the methylation classification first and select path dx and free text based on that. If we want to select free text containing pineoblastoma, I think we need to add more terms in free text and more samples will be included in this module.

[jharenza]

Yea I think let's make the cohort comprehensive; maybe grepl instead of exact matches on all variations of pineoblastoma ?