Using slot instead of layer

[efratsh12]

In wilcoxauc, Using slot instead of layer gives 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.
Run rlang::last_trace() to see where the error occurred.

[konsternacja]

Unfortunately, I have the same problem, but I managed to get around it this way:

wilcoxauc.Seurat <- function(
    X,
    group_by = NULL,
    assay = "data",
    groups_use = NULL,
    seurat_assay = "RNA",
    ...
) {
    requireNamespace("Seurat")
    X_matrix <- Seurat::GetAssayData(X, assay = seurat_assay, layer = assay)
    if (is.null(group_by)) {
        y <- Seurat::Idents(X)
    } else {
        y <- Seurat::FetchData(X, group_by) %>% unlist %>% as.character()
    }
    wilcoxauc(X_matrix, y, groups_use)
}

cl_markers_presto <- wilcoxauc.Seurat(seurat_obj)

It's not perfect, but at least it's usable...