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WPRE_mapping/MAGIC_imputation.R

+library(Seurat)
+library(Rmagic)
+library(ggplot2)
+library(viridis)
+library(dplyr)
+library(ggpubr)
+library(openxlsx)
+
+wdir <- "./WPRE_mapping"
+
+t <- readRDS(paste(wdir, "Full_dataset_counts.rds", sep = "/"))
+
+ss <- stringr::str_split_fixed(colnames(t), pattern = "-", n = 2)[,1] %>% unique()
+full_t <- list()
+for (sample in ss) {
+  print(sample)
+  sample_cells <- grep(paste0(sample, "-"), colnames(t), value = T)
+  t_sample <- t(t[,sample_cells])
+  # keep genes expressed in at least 10 cells
+  keep_cols <- colSums(t_sample > 0) > 10
+  t_sample <- t_sample[,keep_cols]
+  t_sample <- library.size.normalize(t_sample)
+  t_sample <- sqrt(t_sample)
+  t_sample_MAGIC <- magic(t_sample, genes = c("Cd8a","Cd4","Cd3e","Cd14","Mki67","Top2a","TGeneCAR-WPRE"))
+  magic_res <- as.data.frame(t_sample_MAGIC$result)
+  full_t[[sample]] <- magic_res
+}
+saveRDS(object = full_t, file = paste(wdir, "MAGICimputation.rds", sep = "/"))
+
+# Add MAGIC imputation to Seurat meta-data
+df <- data.frame()
+for (sample in names(full_t)) {
+  df_sample <- full_t[[sample]]
+  df_sample$Sample <- sample
+  df <- rbind(df, df_sample)
+}
+full_obj <- readRDS(paste(wdir, "Full_dataset.rds", sep = "/"))
+md <- df[, "TGeneCAR-WPRE", drop = F]
+colnames(md) <- "TGeneCAR_WPRE_MAGIC"
+head(md)
+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)