immune cell survival update to include extent tumor resect + lgg group - Githubissues

AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project

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immune cell survival update to include extent tumor resect + lgg group #1344

Closed jharenza closed 2 years ago

jharenza commented 2 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

Adding extent of tumor resection and lgg grouping per @adamcresnick

What was your approach?

Same as in #1342

What GitHub issue does your pull request address?

NA

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

Which areas should receive a particularly close look?

NA

Is there anything that you want to discuss further?

Removed subtype analysis from here because of #1332 and that this PR only included RNA samples.

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?

pretty much the same as before, except PDL1 expression is not significant across the entire cohort

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

[ ] 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.
[x] The analytical code is documented and contains comments.

sjspielman commented 2 years ago

I'm going to go ahead and merge this in since it's passed CI and been approved!