Error in (function (classes, fdef, mtable) about slingshot HOT 2 CLOSED

Hey @GBeattie,

Thanks for the interest! Unfortunately, Slingshot cannot (currently?) work with Seurat objects, but there are a couple different ways around this:

1. I think the most intuitive solution might be to use Seurat's as.SingleCellExperiment and as.Seurat functions, since Slingshot can work with SingleCellExperiment objects (the code would look identical to what you already have, but sample.combined would be a different class). I say "might be" because I haven't used these functions extensively and there may be some data loss when converting from one type to the other, so just be careful about checking that everything you need is still there!

2. If you don't want to convert everything, you could also pull out the necessary parts of the Seurat object for running Slingshot. Specifically, these would be the PCA coordinates (Reductions(sample.combined, slot = 'PCA'), I think...) and the cluster labels (sample.combined$seurat_clusters). Similarly, you can then extract the pseudotime values from the resulting SlingshotDataSet (via slingPseudotime) and, if you want, add them to the metadata of your Seurat object.

Hope this helps and let me know if anything still doesn't work!

from slingshot.

Converted and seems to be running now, no sign of meta data loss, thanks!

from slingshot.