Update IHG subtyping

[zzgeng]

Purpose/implementation Section

What scientific question is your analysis addressing?

Update molecular-subtyping-HGG module

What was your approach?

Add new subtype IHG, including
IHG, NTRK-altered
IHG, ROS1-altered
IHG, ALK-altered
IHG, MET-altered
IHG, To be classified

What GitHub issue does your pull request address?

d3b-center/ticket-tracker-OPC#474

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

Which areas should receive a particularly close look?

07-HGG-molecular-subtyping-combine-table.Rmd
HGG_cleaned_all_table.tsv

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?

Results

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

Tables

What is your summary of the results?

Add IGH molecular subtype

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 will go through this today, but can you merge update_MET_fusion into this branch when you get a chance? That will allow these PRs to be staggered.

[jharenza]

Hi @zzgeng - can you make the few requested changes and I will continue after that?

[jharenza]

Hi @zzgeng thank you so much for working on this and sorry for the delay in review. I left some comments for making code a bit more concise and a change to use the fusion summary file here.

I also suggested to put all methylation bs_ids in the final table as well.

For the final molecular_subtypes.tsv table, I see fusion evidence is NA for the IHG samples - can you add the fusions to this table?

[jharenza]

just a few typos I noticed

[jharenza]

going to get this in to build into mol #315

[jharenza]

going to merge since this has passed HGG subtyping