Merge datasets

Code

# Enrique Blanco Carmona
# e.blancocarmona@kitz-heidelberg.de
# PhD Student – Clinical Bioinformatics
# Division of Pediatric Neurooncology (B062)
# DKFZ-KiTZ | Germany

#--------------------------------------------------------------------
# 3 - MERGE INDIVIDUAL SAMPLES TOGETHER
#--------------------------------------------------------------------

# Generate a list containing all samples.
list_samples <- list()
sample_names_vector <- c() # Vector containing all sample names.

for (sample_name_use in sample_names_vector){
    sample.individual <- readRDS(paste0(output_path, "/", sample_name_use, "_after_QC.rds"))
    list.samples[[sample_name_use]] <- sample.individual
}

# Generate the merged sample.
sample_name <- "" # Name for the merged sample.
sample <- merge(list_samples[[1]],
                y = list_samples[2: length(list_samples)],
                add.cell.ids = names(list_samples),
                project = sample_name)

merged_sample@meta.data$orig.ident <- stringr::str_replace_all(merged_sample@meta.data$orig.ident, "\\.", "-")

# Exclude doublets.
message(print0("Total number of doublets in the sample: ", sum(sample$scrublet_binary)))
sample <- sample[, sample$scrublet_binary == FALSE]