From 95dd3a1f03a7ead013aef5f88e1983efbfa84c0f Mon Sep 17 00:00:00 2001
From: lahuuki <lahuuki@gmail.com>
Date: Wed, 10 Sep 2025 12:22:16 -0400
Subject: [PATCH] If gene_name and gene_id are in rowData, add gene_search as
 defined in check_sce_layer

---
 R/registration_pseudobulk.R    | 9 ++++++++-
 man/registration_pseudobulk.Rd | 3 ++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/R/registration_pseudobulk.R b/R/registration_pseudobulk.R
index ffec8c4c..dcbcb8e6 100644
--- a/R/registration_pseudobulk.R
+++ b/R/registration_pseudobulk.R
@@ -57,7 +57,7 @@
 #' sce$age <- ages[sce$sample_id]
 #'
 #' ## Add gene-level information
-#' rowData(sce)$ensembl <- paste0("ENSG", seq_len(nrow(sce)))
+#' rowData(sce)$gene_id <- paste0("ENSG", seq_len(nrow(sce)))
 #' rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))
 #'
 #' ## Pseudo-bulk by Cell Cycle
@@ -69,6 +69,7 @@
 #'     min_ncells = NULL
 #' )
 #' colData(sce_pseudo)
+#' rowData(sce_pseudo)
 registration_pseudobulk <-
     function(
         sce,
@@ -230,6 +231,12 @@ registration_pseudobulk <-
             spatialCoords(sce_pseudo) <- NULL
             imgData(sce_pseudo) <- NULL
         }
+        
+        ## if gene_anme and gene_id cols are available add gene_search to rowData
+        if(all(c("gene_name", "gene_id") %in% colnames(rowData(sce_pseudo)))){
+        rowData(sce_pseudo)$gene_search <- paste0(rowData(sce_pseudo)$gene_name, "; ", rowData(sce_pseudo)$gene_id)
+        }
+
         if (!is.null(pseudobulk_rds_file)) {
             message(Sys.time(), " saving sce_pseudo to ", pseudobulk_rds_file)
             saveRDS(sce_pseudo, file = pseudobulk_rds_file)
diff --git a/man/registration_pseudobulk.Rd b/man/registration_pseudobulk.Rd
index 8d486941..8b8dd22a 100644
--- a/man/registration_pseudobulk.Rd
+++ b/man/registration_pseudobulk.Rd
@@ -76,7 +76,7 @@ names(ages) <- LETTERS[1:5]
 sce$age <- ages[sce$sample_id]
 
 ## Add gene-level information
-rowData(sce)$ensembl <- paste0("ENSG", seq_len(nrow(sce)))
+rowData(sce)$gene_id <- paste0("ENSG", seq_len(nrow(sce)))
 rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))
 
 ## Pseudo-bulk by Cell Cycle
@@ -88,6 +88,7 @@ sce_pseudo <- registration_pseudobulk(
     min_ncells = NULL
 )
 colData(sce_pseudo)
+rowData(sce_pseudo)
 }
 \seealso{
 Other spatial registration and statistical modeling functions: