assay name

stemangiola · Jul 24, 2024 · 6a0ec5b · 6a0ec5b
1 parent 923de59
commit 6a0ec5b
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/R/import_metadata_and_counts.R b/R/import_metadata_and_counts.R
@@ -146,15 +146,16 @@ import_one_sce <- function(
     cli_alert_info("Generating pseudobulk counts from {file_id}. ")
     pseudobulk_counts <- sce_obj |> aggregate_cells(c(sample_, cell_type_harmonised)) 
 
-    normalised_counts_best_distribution <- assay(pseudobulk_counts, "counts") |> as.matrix() |>
+    assay_name <- pseudobulk_counts |> assays() |> names()
+    normalised_counts_best_distribution <- assay(pseudobulk_counts, assay_name) |> as.matrix() |>
       preprocessCore::normalize.quantiles.determine.target()
 
     normalised_counts <- pseudobulk_counts |> quantile_normalise_abundance(
       method="preprocesscore_normalize_quantiles_use_target",
       target_distribution = normalised_counts_best_distribution
     )
 
-    assay(normalised_counts, "counts") <- NULL
+    assay(normalised_counts, assay_name) <- NULL
     names(assays(normalised_counts)) <- "quantile_normalised"
 
     if (!dir.exists(file.path(cache_dir, "pseudobulk/original"))) {