Seurat 5 integration

Question

[sarahmanderni]

In Seurat 5 vignette the integration is performed as streamlined (one-line) and there is no information on how to set the parameters example number of PCs (ndims) or number of variable features to use for integration. Do you run the function in default format or do you set these parameters as before (e.g. after checking for elbow plots etc).

Answer 1

[jared.andrews07]

You are still free to change whichever parameters you want for whichever method you're using. See ?IntegrateLayers and whichever method you're using, e.g. ?CCAIntegration.