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process_vireo_sce: Integrate Vireo donor assignments with a SingleCellExperiment object

process_vireo_sce.Rd

Processes donor genetic identity data from Vireo and integrates it with a SingleCellExperiment object's metadata. The function adds donor assignments to the colData, matches cell identifiers between Vireo output and the SCE object, and generates summary statistics of cell type distributions per donor.

Arguments

sce_obj

A SingleCellExperiment object. The single-cell dataset to be annotated with donor information.

vireo_path

Character. Path to the Vireo donor_ids.tsv file containing donor assignments.

prefix_text

Character. Text to prepend to cell identifiers in the Vireo data to match the cell barcodes in the SingleCellExperiment object.

Value

A list containing:

sce_object

The SingleCellExperiment object with donor assignment metadata added

donor_data

Data frame containing donor assignments for matched cells

matching_cells

Character vector of cell identifiers that matched between SCE and Vireo

summaries

List of summary statistics including:

  • donor_summaries: Per-donor cell counts and cell type distributions (if available)

  • cells_matched: Total number of cells successfully matched

  • total_sce_cells: Total number of cells in the SingleCellExperiment object

  • total_vireo_cells: Total number of cells in the Vireo data

Details

This function first processes the Vireo TSV file using the process_tsv function, adding the prefix to cell identifiers. It then adds the donor assignments to the SingleCellExperiment object's colData and generates summary statistics of cell type distributions for each donor (if cell_type information is available in colData).

Note

The function checks for a "cell_type" column in the SingleCellExperiment object's colData. If present, it will generate cell type distribution summaries per donor. If not, the cell_types field in donor_summaries will be NULL.

Examples

if (FALSE) { # \dontrun{
# Process a SingleCellExperiment object with Vireo donor assignments
results <- process_vireo_sce(
  sce_obj = my_sce_object,
  vireo_path = "path/to/vireo/donor_ids.tsv",
  prefix_text = "Patient1_Sample3_"
)

# Access the updated SingleCellExperiment object
updated_sce <- results$sce_object

# Check matching statistics
results$summaries$cells_matched
results$summaries$total_sce_cells
} # }