AlexsLemonade / AlexsLemonade/scpcaTools
Account for altExp when converting SCE to AnnData
- Dominant language
- R
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Description
In the function to convert from SCE to AnnData, any data stored as an `altExp` will not be converted. It does not appear that AnnData has much functionality for additional multi-omics data, but I did find this [tutorial](https://scanpy-tutorials.readthedocs.io/en/multiomics/cite-seq/pbmc5k.html) that we could use as a reference. Also see some additional thoughts below regarding ways to handle the multi-omics data.
> The one remaining thing that you mentioned in your initial comments was the handling of alt experiments. I agree that it is correct to make that a separate issue, but I wanted to put some thoughts here while I am thinking about it. It looks to me that AnnData can't really handle those at this point except by adding the additional measures as "genes" and then annotating them in the metadata. I don't love that solution, as I think it puts an odd burden on the user to know that the matrix has other data. I think the best solution for now may be to simply output multiple AnnData objects, one for each modality. There is the [`MuData` class](https://github.com/scverse/muon) which wraps up multiple AnnData objects, but I am not sure how easy the support within R will be, or whether that would really be worth the effort.
_Originally posted by @jashapiro in https://github.com/AlexsLemonade/scpcaTools/pull/114#pullrequestreview-1032897579_
Contributor guide
Research direction
Start at the SCE-to-AnnData conversion function and review how altExp data is represented. Compare the options described in the issue with the linked Scanpy multi-omics tutorial and consider the MuData reference. Done means altExp content is converted using an agreed representation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100