V23 integrate (9/n)

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

What was your approach?

• Add a notebook for RNA extraction type 00-prepare-extraction-table.Rmd
• Update 01-integrate-subtyping.Rmd to add the extraction_type to base_histology and then to pbta-histologies.tsv
• Rerun module to get finalized histology file.

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?

Is there anything that you want to discuss further?

Double check the extraction status looks OK and if this is sufficient for downstream work/ any modifications are suggested.

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)?

pbta_extraction_status pbta-histologies.tsv also has the newly subtyped YAP1 EPN samples now

What is your summary of the results?

Same extraction 910         
Different tissue aliquot    49          
Same tissue aliquot 44          
NA  11  

Reproducibility Checklist

• [x] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• [x] This analysis has been added to continuous integration.

Documentation Checklist

• [x] This analysis module has a README and it is up to date.
• [x] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• [x] The analytical code is documented and contains comments.

[jharenza]

Although a private repo, I am tracking here that the upstream data wrangling for the *aliquots.tsv files has been submitted in PR here and will be reviewed by @ewafula. @ewafula please comment here after you have a chance to review! Thanks.

[ewafula]

@jharenza, I'll work to review. Hopefully will donentomorrow AM.

[jharenza]

@jaclyn-taroni I also found an instance in which the aliquot id was broken up for 7316-135 into 3 different IDs when doing the search for parental aliquot upstream, so I updated that sample in the CBTN file as well. Ready for re-review.