Exploratory CNV notebook for Wilms tumor annotation (SCPCP000014)

[JingxuanChen7]

Purpose/implementation Section

Please link to the GitHub issue that this pull request addresses.

Analysis proposal: #628
Issue: #812
Other related discussion: #808

What is the goal of this pull request?

I planned to identify tumor cells from normal cells, which could also help improve the annotation for normal cells. To start with, I tried inferCNV and copyKat using sample SCPCL000850, which shows more divergent cell compartments, and a relatively clearer annotation compared with others. Since the results are not quite positive, here I would add this analysis for record as notebook rather than adding into the main pipeline.

Briefly describe the general approach you took to achieve this goal.

inferCNV and copyKat on sample SCPCL000850.

If known, do you anticipate filing additional pull requests to complete this analysis module?

N.A.

Results

What is the name of your results bucket on S3?

Results for this PR won't be uploaded to S3.

What types of results does your code produce (e.g., table, figure)?

Rendered R notebook in .html format.

What is your summary of the results?

For CopyKat, we observed inconsistent results with or without reference normal cells.

For inferCNV, we could observe clear Chr1p gain and Chr11 loss across almost all fetal_nephron. However, we couldn't observe much normal cell subgroups as contrast. The possibility that fetal_nephron cells are all tumor related could explain our results, which is, however, hard to validate.

Provide directions for reviewers

What are the software and computational requirements needed to be able to run the code in this PR?

• Analysis could be executed on a virtual computer (Standard-4XL) via AWS Lightsail for Research.
• Required R packages checked in renv.lock file.

Are there particularly areas you'd like reviewers to have a close look at?

NA

Is there anything that you want to discuss further?

NA

Author checklists

Analysis module and review

• This analysis module uses the analysis template and has the expected directory structure.
• The analysis module README.md has been updated to reflect code changes in this pull request.
• The analytical code is documented and contains comments.
• Any results and/or plots this code produces have been added to your S3 bucket for review.

Reproducibility checklist

• Code in this pull request has been added to the GitHub Action workflow that runs this module.
• The dependencies required to run the code in this pull request have been added to the analysis module Dockerfile.
• If applicable, the dependencies required to run the code in this pull request have been added to the analysis module conda environment.yml file.
• If applicable, R package dependencies required to run the code in this pull request have been added to the analysis module renv.lock file.

[sjspielman]

Hi @JingxuanChen7, thanks for writing up this exploratory analysis in a PR! Overall, the code looks like it's in good shape, so I wanted to just give you an update about review - I'm working now to run the code, so once that is done, I'll return with any more comments I have.

In addition, I think it would be good to place this exploratory analysis in a subdirectory named exploratory_analysis/03_cnv (or similar). This way, if there are more exploratory analyses, we won't have too many files for different analyses in the same place. I recommend keeping an overall exploratory_analysis/README.md that just explains this folder contains exploratory analyses and lists them out (for now, just this one!), and the information you currently have in that readme can be copied into exploratory_analysis/03_cnv/README.md. You will have to modify paths here as well when you copy the readme code, including the path to the cell-type-ewings script. Please let me know if I can clarify any of this! :)

[sjspielman]

I've successfully been able to run through all the exploratory analysis code 🎉! Once you are able to implement the additional reviews I left, this should be good to go 😄 . Let me know if I can clarify any of my comments or if you have other questions you want to discuss!

[sjspielman]

Looks great @JingxuanChen7, thanks for making those changes! I'll go ahead and approve and get this merged into main 🚀