tcga_partition_barcodes.R

partition_barcodes_by_sample_type <- function(barcodes) {
  # Define a list to store partitioned barcodes by sample type names
  ## Example usage
  ## barcodes <- c("TCGA-02-0001-01C-01D-0182-01", "TCGA-02-0002-02C-01D-0182-01", "TCGA-02-0003-03C-01D-0182-01", "TCGA-02-0001-01C-01D-0182-02")
  ## partitioned_barcodes <- partition_barcodes_by_sample_type(barcodes)
  ## print(partitioned_barcodes)



  sample_type_names <- list(
    "01" = "primary_solid_tumor",
    "02" = "recurrent_solid_tumor",
    "03" = "primary_blood_derived_cancer_peripheral_blood",
    "04" = "recurrent_blood_derived_cancer_bone_marrow",
    "05" = "additional_new_primary",
    "06" = "metastatic",
    "07" = "additional_metastatic",
    "08" = "human_tumor_original_cells",
    "09" = "primary_blood_derived_cancer_bone_marrow",
    "10" = "blood_derived_normal",
    "11" = "solid_tissue_normal",
    "12" = "buccal_cell_normal",
    "13" = "ebv_immortalized_normal",
    "14" = "bone_marrow_normal",
    "15" = "sample_type_15",
    "16" = "sample_type_16",
    "20" = "control_analyte",
    "40" = "recurrent_blood_derived_cancer_peripheral_blood",
    "50" = "cell_lines",
    "60" = "primary_xenograft_tissue",
    "61" = "cell_line_derived_xenograft_tissue",
    "99" = "sample_type_99"
  )

  partitioned_barcodes <- list()
  patient_samples <- list()

  # Extract sample type code from each barcode
  for (barcode in barcodes) {
    sample_type_code <- substr(barcode, 14, 15)
    patient_id <- substr(barcode, 9, 12)
    sample_type_name <- sample_type_names[[sample_type_code]]

    if (is.null(sample_type_name)) {
      warning(paste("Unknown sample type code:", sample_type_code))
      next
    }

    # Initialize a list for the sample type name if it doesn't exist
    if (!sample_type_name %in% names(partitioned_barcodes)) {
      partitioned_barcodes[[sample_type_name]] <- list()
    }

    # Append the barcode to the corresponding sample type name list
    partitioned_barcodes[[sample_type_name]] <- c(partitioned_barcodes[[sample_type_name]], barcode)

    # Track patient samples to detect duplicates
    if (!patient_id %in% names(patient_samples)) {
      patient_samples[[patient_id]] <- list()
    }

    if (!sample_type_name %in% names(patient_samples[[patient_id]])) {
      patient_samples[[patient_id]][[sample_type_name]] <- list()
    }

    patient_samples[[patient_id]][[sample_type_name]] <- c(patient_samples[[patient_id]][[sample_type_name]], barcode)

    # Warning for multiple samples of the same type from the same patient
    if (length(patient_samples[[patient_id]][[sample_type_name]]) > 1) {
      warning(paste("Multiple samples of the same type for patient", patient_id, ":", sample_type_name))
    }
  }

  return(partitioned_barcodes)
}