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process_vireo_dataframe: Integrate Vireo donor assignments with a metadata data frame

process_vireo_dataframe.Rd

Processes donor genetic identity data from Vireo and integrates it with an existing metadata data frame. The function matches cell identifiers between the Vireo output and the metadata, and generates basic cell count statistics per donor.

Arguments

metadata_df

A data frame. The metadata data frame to match with donor information, with cell identifiers as row names.

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 identifiers in the metadata data frame.

Value

A list containing:

metadata

The original metadata data frame, unchanged

donor_data

Data frame containing donor assignments for matched cells

matching_cells

Character vector of cell identifiers that matched between metadata and Vireo

summaries

List of summary statistics including:

  • donor_summaries: Per-donor cell counts

  • cells_matched: Total number of cells successfully matched

  • total_cells: Total number of cells in the metadata data frame

  • total_vireo_cells: Total number of cells in the Vireo data

Details

This function provides a simpler alternative to the Seurat and SingleCellExperiment integrations when you only have a data frame of metadata. It first processes the Vireo TSV file using the process_tsv function, adding the prefix to cell identifiers, then finds matching cells between the Vireo data and the metadata data frame, and generates basic summary statistics.

Note

Unlike the Seurat and SingleCellExperiment integration functions, this function does not modify the input metadata data frame. It only returns the matching information.

Examples

if (FALSE) { # \dontrun{
# Process a metadata data frame with Vireo donor assignments
results <- process_vireo_dataframe(
  metadata_df = cell_metadata,
  vireo_path = "path/to/vireo/donor_ids.tsv",
  prefix_text = "Patient1_Sample3_"
)

# Check matching statistics
results$summaries$cells_matched
results$summaries$total_cells

# Access donor assignments for matched cells
donor_assignments <- results$donor_data
} # }