Update MAGIC_imputation.R

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)
+