@@ -321,6 +321,7 @@ clustify.Seurat <- function(input,

     per_cell = FALSE,

     n_perm = 0,

     compute_method = "spearman",

+    pseudobulk_method = "mean",

     use_var_genes = TRUE,

     dr = "umap",

     seurat_out = TRUE,

@@ -369,6 +370,7 @@ clustify.Seurat <- function(input,

         n_perm = n_perm,

         cluster_col = cluster_col,

         compute_method = compute_method,

+        pseudobulk_method = pseudobulk_method,

         verbose = verbose,

         rm0 = rm0,

         exclude_genes = exclude_genes,

@@ -444,6 +446,7 @@ clustify.SingleCellExperiment <- function(input,

     per_cell = FALSE,

     n_perm = 0,

     compute_method = "spearman",

+    pseudobulk_method = "mean",

     use_var_genes = TRUE,

     dr = "umap",

     seurat_out = TRUE,

@@ -488,6 +491,7 @@ clustify.SingleCellExperiment <- function(input,

         n_perm = n_perm,

         cluster_col = cluster_col,

         compute_method = compute_method,

+        pseudobulk_method = pseudobulk_method,

         verbose = verbose,

         rm0 = rm0,

         exclude_genes = exclude_genes,

@@ -47,6 +47,7 @@ clustify(input, ...)

   per_cell = FALSE,

   n_perm = 0,

   compute_method = "spearman",

+  pseudobulk_method = "mean",

   use_var_genes = TRUE,

   dr = "umap",

   seurat_out = TRUE,

@@ -73,6 +74,7 @@ clustify(input, ...)

   per_cell = FALSE,

   n_perm = 0,

   compute_method = "spearman",

+  pseudobulk_method = "mean",

   use_var_genes = TRUE,

   dr = "umap",

   seurat_out = TRUE,