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feiyoung / PRECAST

an efficient data integration method for multiple spatial transcriptomics data with non- cluster-relevant effects such as the complex batch effects.
GNU General Public License v3.0
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Possible Incompatiblity with Seurat V5 #12

Closed boyiguo1 closed 1 year ago

boyiguo1 commented 1 year ago

I wonder if you have tested your implementation with Seurat V5.

It seems that Seurat V5 used a new data structure (Assay (v5) data, https://satijalab.org/seurat/articles/seurat5_essential_commands.html#working-with-layers) to count matrices, which seems to break your current implementation when feeding CreatePRECASTObject a seuList created using Seurat V5.

> preobj <- CreatePRECASTObject(seuList = seuList)
Filter spots and features from Raw count data...
  |                                                  | 0 % ~calculating  Error in FUN(X[[i]], ...) : 
  no slot of name "counts" for this object of class "Assay5"

Specifically

> seuList[[1]][["RNA"]]@counts
Error: no slot of name "counts" for this object of class "Assay5"

For your information, I am using Seurat_4.9.9.9049

feiyoung commented 1 year ago

Thank you for your feedback! I'll fix it in recent days.

feiyoung commented 1 year ago

Now, PRECAST version 1.6.2 supports the Seurat V5.

Thank you!