AlexsLemonade / AlexsLemonade/sc-data-integration

seurat integration investigation

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Description

I'm reviving this comment for (optional, mostly for curiosity) discussion: https://github.com/AlexsLemonade/sc-data-integration/pull/77#issuecomment-1205752496

...because I have now encountered the pseudo-error (since execution doesn't actually stop!) `Error in x$.self$finalize() : attempt to apply non-function` in a whole other context that might be useful for us to know. When doing some unit tests over in https://github.com/AlexsLemonade/scpcaTools/pull/157, I encountered this error message when running `expect_warning()` and _not_ saving the object within. In other words:
- `expect_warning( run_thing() )` ---> error
- `expect_warning( result <- run_thing() )` ---> no error

So, I'm going to say that Seurat is doing some kind of analogous operation internally, not capturing output that doesn't matter, and we are seeing the resulting error. Notably I have done 0 spelunking to back this theory up.

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Research direction

Start by reading the linked comment on pull request 77 and the scpcaTools pull request 157, then reproduce the contrasting expect_warning(run_thing()) cases described here. Done would be a documented determination of whether Seurat exhibits the analogous behavior and what the investigation found.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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