Skip to contents

process_vireo_seurat: Integrate Vireo donor assignments with a Seurat object

process_vireo_seurat.Rd

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

Arguments

seurat_obj

A Seurat 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 Seurat object.

Value

A list containing:

seurat_object

The Seurat 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 Seurat and Vireo

summaries

List of summary statistics including:

  • donor_summaries: Per-donor cell counts and cell type distributions

  • cells_matched: Total number of cells successfully matched

  • total_seurat_cells: Total number of cells in the Seurat 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 Seurat object's metadata and generates summary statistics of cell type distributions for each donor. The function prints verbose diagnostic information during execution to help track the matching process.

Note

The function assumes that the Seurat object has a "cell_type" column in its metadata, which is used to generate the cell type distribution summaries per donor.

Examples

if (FALSE) { # \dontrun{
# Process a Seurat object with Vireo donor assignments
results <- process_vireo_seurat(
  seurat_obj = my_seurat_object,
  vireo_path = "path/to/vireo/donor_ids.tsv",
  prefix_text = "Patient1_Sample3_"
)

# Access the updated Seurat object
updated_seurat <- results$seurat_object

# View donor summaries
results$summaries$donor_summaries

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