AlexsLemonade / AlexsLemonade/scpcaTools

Do we need `cluster_sce()`?

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#212 2 comments 0 reactions 0 assignees View on GitHub
Dominant language
R
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Description

I just noted that there is already a function `scran::clusterCells()` which does almost everything we do with `cluster_sce()`, with the exception being saving the results back to a separate SCE object.

Since we can add the cluster info with a line like:

```
sce$clusters <- scran::clusterCells(
sce,
use.dimred = "PCA",
BLUSPARAM=NNGraphParam(k=15)
)
```

are we sure we need our own version of the function?

Contributor guide

Open the contributing guide

Research direction

Start by locating scpcaTools' cluster_sce() and comparing its behavior with scran::clusterCells(), especially the separate SCE result mentioned in the issue. Review the two existing comments and determine whether the project should retain, replace, or remove the wrapper; done means the decision and resulting scope are documented.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Refactor
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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