Previously missing PB subtypes added #601
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jharenza
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analyses/molecular-subtyping-PB/01-molecular-subtype-pineoblastoma.Rmd
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hi @sangeetashukla I left some comments for changes required here
Hi @jharenza I have made the changes. Please take a look when you can. |
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hi @sangeetashukla thanks for the update. I found a bug where the low conf methyl subtypes were being propagated and pushed a commit for that. This looks good now, no new samples subtyped but the code exists now. Let's see if it passes.
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Purpose/implementation Section
Add PPTID subtypes
What scientific question is your analysis addressing?
There were some PPT ID subtypes that were not added to the module earlier. The module needed updates to include those additional subtypes.
What was your approach?
Review the input data source to ascertain which subtypes were missed.
Correctly map the pathology_free_text_diagnosis to molecular_subtype_methyl
Followed by mapping molecular_subtype correctly
Run the module to re-generate subtypes in the results/ directory
What GitHub issue does your pull request address?
Issue 590
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Please review the subtypes for their acceptable nomenclature
Is there anything that you want to discuss further?
No
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)?
What is your summary of the results?
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.