Seurat v5 Compatibility Issues
Environment
- R 4.5, Seurat v5.x, miRTalk v1.0.0, macOS (Apple Silicon)
Issue 1: create_miRTalk() fails with Assay5 class
AddModuleScore() fails internally because [[<- assignment is incompatible with the new Seurat v5 Assay5 object structure.
Warning: No layers found matching search pattern provided
Error in `[[<-`(`*tmp*`, colnames(x = features.scores.use), value = features.scores.use) :
[[<- defined for objects of type "S4" only for subclasses of environment
Issue 2: find_hvtg() fails accessing @meta.data slot
The line sc_data@assays[["RNA"]]@meta.data[["var.features"]] does not work in Seurat v5 — the @meta.data slot does not exist on the Assay object in v5.
Error in find_hvtg(object = obj) :
no slot of name "meta.data" for this object of class "Assay"
Seurat v5 Compatibility Issues
Environment
Issue 1:
create_miRTalk()fails with Assay5 classAddModuleScore()fails internally because[[<-assignment is incompatible with the new Seurat v5Assay5object structure.Issue 2:
find_hvtg()fails accessing@meta.dataslotThe line
sc_data@assays[["RNA"]]@meta.data[["var.features"]]does not work in Seurat v5 — the@meta.dataslot does not exist on the Assay object in v5.