From 03af214987673cd22bd6e7381435dfe8f6dad803 Mon Sep 17 00:00:00 2001 From: Stefano Beretta Date: Wed, 26 Feb 2025 14:32:50 +0000 Subject: [PATCH] Update MAGIC_imputation.R --- WPRE_mapping/MAGIC_imputation.R | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/WPRE_mapping/MAGIC_imputation.R b/WPRE_mapping/MAGIC_imputation.R index 6047784..bcb4ae0 100644 --- a/WPRE_mapping/MAGIC_imputation.R +++ b/WPRE_mapping/MAGIC_imputation.R @@ -43,3 +43,13 @@ full_obj <- AddMetaData(object = full_obj, metadata = md) # Add WPRE counts to Seurat meta-data wpre_expr <- data.frame("TGeneCAR_WPRE_count" = full_obj@assays$RNA@counts["TGeneCAR-WPRE",]) full_obj <- AddMetaData(object = full_obj, metadata = wpre_expr) + +# Select CART +df <- FetchData(object = full_obj, c("UMAPh_1", "UMAPh_2", colnames(full_obj@meta.data))) +sel_thr <- 0.05 +df <- mutate(df_final, CART_MAGIC = ifelse(df$Annotation %in% c("MemoryT","ActivatedT","EffectorCd8", "CtlsT","IfnT","GammaDelta","StemLikeT") &df$TGeneCAR_WPRE_MAGIC >= sel_thr, "CART_MAGIC", "NA")) +df_cart <- df[, "CART_MAGIC", drop = F] +full_obj@misc$analysis_params[["CART_MAGIC_thr"]] <- sel_thr +full_obj@meta.data$CART_MAGIC <- NULL +full_obj <- AddMetaData(object = full_obj, metadata = df_final_cart) + -- GitLab