Analysis update: Add methylation in LGAT workflow

zzgeng commented 8 months ago

Purpose/implementation Section

What scientific question is your analysis addressing?

Add methylation in LGAT workflow

What was your approach?

Add methylation in LGAT workflow

What GitHub issue does your pull request address?

https://github.com/d3b-center/OpenPedCan-analysis/issues/533

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

Which areas should receive a particularly close look?

molecular subtype lgg module, workflow

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)?

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 commented 8 months ago

Thanks @zzgeng for putting this together. Are we missing some methyl subtypes?

https://github.com/d3b-center/OpenPedCan-analysis/blob/dfe6d9f0ec8ea390f7bd102e8218642971e9299c/analyses/molecular-subtyping-LGAT/01-subset-files-for-LGAT.Rmd#L348-L360

zzgeng commented 8 months ago

Thanks @zzgeng for putting this together. Are we missing some methyl subtypes?

https://github.com/d3b-center/OpenPedCan-analysis/blob/dfe6d9f0ec8ea390f7bd102e8218642971e9299c/analyses/molecular-subtyping-LGAT/01-subset-files-for-LGAT.Rmd#L348-L360

I checked the results and find out I missed one subtype (SEGA, to be classified). I just updated the workflow

jharenza commented 8 months ago

I meant that we need to include all of the above methyl subtypes in the flow - if they were not subtyped by something else, they are via methyl per

https://github.com/d3b-center/OpenPedCan-analysis/blob/dfe6d9f0ec8ea390f7bd102e8218642971e9299c/analyses/molecular-subtyping-LGAT/04-LGAT-compile-subtypes.Rmd#L380-L383

jharenza commented 7 months ago

docs only

d3b-center / OpenPedCan-analysis