Submission table for cell type and tumor classification of ETP T-ALL (SCPCP000003)

[UTSouthwesternDSSR]

Purpose/implementation Section

For the submission of cell type and tumor annotation for ETP T-ALL samples (n=31) in SCPCP000003

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

#822

What is the goal of this pull request?

To submit the cell type and tumor annotation for ETP T-ALL samples (n=31) in SCPCP000003

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

The same approach is followed as proposed in the module for non-ETP T-ALL (SCPCP000003):

• fine-tune B cells by using the 99 percentile cutoff of non-B ScType score in the annotated B cells from ScType
• rerun CopyKat with these fine-tuned B cells as the normal

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

No

Results

What is the name of your results bucket on S3?

s3://researcher-650251722463-us-east-2/cell-type-ETP-ALL-03/

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

What is your summary of the results?

Compared to previous PR, I added the scripts and results for ScType exploration (we then fine-tuned the B cells using the stringent cutoff), running CopyKat and InferCNV using the fine-tuned B cells. As we mention in #838, I will just use CopyKat prediction as the tumor cell classification. The fine-tuning strategy actually help us to purify the B cells in the 4 samples (SCPCL000055, SCPCL000066, SCPCL000696, and SCPCL000709) mentioned in #826, instead of doing manual checking on the location of B cells on umap and comparing them with the BFeatures1 (average expression of B marker genes) on the dotplot.

I also generated the tsv files for the final submission table and png showing the cell type and tumor cell classification (s3://researcher-650251722463-us-east-2/cell-type-ETP-ALL-03/results/submission_table)

Provide directions for reviewers

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

• The packages are installed and updated in renv.lock and conda.lock.
• Analysis could be executed on a Standard-4XL virtual machine via AWS Lightsail for Research

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

Is there anything that you want to discuss further?

Author checklists

Check all those that apply.
Note that you may find it easier to check off these items after the pull request is actually filed.

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.

[jaclyn-taroni]

Thanks, @UTSouthwesternDSSR. I will look at this today since I expect much of this code to be the same as the cell-type-nonETP-ALL-03 module. However, we won't be able to review pull requests of this size in the future; we would require you to break it up into multiple PRs that are more manageable in size. If I'm wrong about the level of repetition, and a lot of this code has yet to be seen before, we will need to break it up.

[UTSouthwesternDSSR]

Sure, sorry about it! It is exactly the same script that I used in cell-type-nonETP-ALL-03 module. I just copy and paste the script here, and changing the directory and sample name.

[jaclyn-taroni]

I have confirmed that the code is largely the same as the cell-type-nonETP-ALL-03 module and that the submission tables are present for all 31 samples in the bucket, so I am marking this as approved.