Could possibly adding support to Seurat V5

[HarrisHan2k]

Hi there,

I meet a "GetAssayData" error, when applying the progeny function to a Seurat object under Seurat V5 conditions.

Here is the error:

"Error:
! The slot argument of GetAssayData() was deprecated in SeuratObject 5.0.0 and is now defunct.
ℹ Please use the layer argument instead.
Traceback:

1. progeny.Seurat(cdc2.object, scale = FALSE, organism = "Human",
   . top = 500, perm = 1, return_assay = TRUE)
2. progeny(as.matrix(Seurat::GetAssayData(expr, slot = "data", assay = assay_name)),
   . scale = scale, organism = organism, top = top, perm = perm,
   . verbose = verbose, z_scores = z_scores, get_nulldist = get_nulldist,
   . assay_name = assay_name, return_assay = return_assay)
3. as.matrix(Seurat::GetAssayData(expr, slot = "data", assay = assay_name))
4. Seurat::GetAssayData(expr, slot = "data", assay = assay_name)
5. GetAssayData.Seurat(expr, slot = "data", assay = assay_name)
6. .Deprecate(when = "5.0.0", what = "GetAssayData(slot = )", with = "GetAssayData(layer = )")
7. deprecate_stop(when = wv, what = what, with = with, env = caller,
   . ...)
8. deprecate_stop0(msg)
9. cnd_signal(error_cnd(c("lifecycle_error_deprecated", "defunctError"),
   . old = NULL, new = NULL, package = NULL, message = msg))
10. signal_abort(cnd)
11. signalCondition(cnd)"

Could you please help modify the codes to get the assay using another method, or adding a if-else sentence?

[nemke333]

I have the same issue would be great to get this patched!

[zhang163yv-pixel]

use function :as.matrix