Running alra in integrated data

[kvshams]

Hi,
Thank you for the great functions for Seurat and making life more easy. Is it possible to run alra on integrated data by preserving the conditions, ie something like RunALRA(object, split.by="Treatment") ?

[mojaveazure]

Currently, RunALRA does not support a split.by argument. If this is a feature you'd like, I'd suggest bringing it up with the authors of RunALRA

[kvshams]

I have already enquired the same in ALRA Github page. The moderator suggested to follow this method but not sure how to do it on Seurat.

[mojaveazure]

We wouldn't recommend running ALRA on the integrated data. If you want to integrate on the imputed data, you can run ALRA on each initial object (or split a merged Seurat object with SplitObject), then integrate each component object.