AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Add function to create total CNV column

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analysis
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3d 5h
Merged PRs (30d)
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Description

### If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.

Part of #1143

### Describe the goals of the changes to the analysis module.

We have this function in the exploratory notebooks in the `infercnv-consensus-cell-type` module appearing in multiple exploratory notebooks:

https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/47d218829b4fc0375cb4b9798784ab85db8b3c2f/analyses/infercnv-consensus-cell-type/exploratory-notebooks/02_ewings-reference-cnv.Rmd#L34-L62

When we return to working on this module for neuroblastoma samples, we should move this function into its own utils file to keep things modular since we anticipate using it more in the future.

### What will your pull request contain?

New utils file with functions that are imported in relevant notebooks

### Will you require additional software beyond what is already in the analysis module?

No

### Will you require different computational resources beyond what the analysis module already uses?

No

### If known, when do you expect to file the pull request?

_No response_

Contributor guide

Open the contributing guide

Research direction

Start with analyses/infercnv-consensus-cell-type/exploratory-notebooks/02_ewings-reference-cnv.Rmd, especially the function at lines 34-62, and inspect the other exploratory notebooks where it appears. Create the proposed utils file and update the relevant notebooks to import the shared function; done means the duplicated function is centralized for future neuroblastoma work.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
bioinformatics
Issue type
Refactor
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
48/100

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