Update ATRT subtype

[zzgeng]

Purpose/implementation Section

UPDATED Analysis: ATRT subtyping

What scientific question is your analysis addressing?

Assign ATRT tumors to one of 3 subtypes:

ATRT, MYC
ATRT, SHH
ATRT, TYR
using methylation results

What was your approach?

archive current scripts 00, 01, and 02 - create an archive folder and move them there - we might want to use some of this information later for classification in the absence of methylation, but for now, we will rely only on methylation results
Create a subtyping script to subtype all PBTA and/or DGD tumor biospecimens which have matched methylation (matched on sample_id). If methylation does not exist for any ATRT samples, those biospecimens can be deemed "ATRT, To be clasified" subtype.
The above subtypes should be listed in the methylation results (similar to IHG subtyping). Use only those with scores >=0.8.
The expected table will have matched tumor DNA/RNA/methylation biospecimen IDS for all ATRTs with new subtypes or a To be classified subtype.

What GitHub issue does your pull request address?

d3b-center/ticket-tracker-OPC#496

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

Which areas should receive a particularly close look?

OpenPedCan-analysis/analyses/molecular-subtyping-ATRT/ATRT_subtyping.R

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

OpenPedCan-analysis/analyses/molecular-subtyping-ATRT/results/ATRT_subtype_methylation.tsv

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.

[jharenza]

@zzgeng it looks like you have some files pulled over from your last set of PRs, can you update this with the DEV version of the fusion summary files?

Also, can you update the YAML file here to add the ATRT subtyping module? Thanks!

[jharenza]

@zzgeng can you make the bash script in the ATRT subtyping module executable

[jharenza]

Also, just to be consistent with all other modules, can you lowercase the A in Archive folder? Thanks!

[jharenza]

@zzgeng if this passes, we are good to go - updated the bash script to be executable and removed some unnecessary filter steps. I also noticed we were not collecting DGD samples in the final file, so added those to get the full cohort of ATRT here.