Assign clonotypes by mapping to a reference table — assign_clonotype_from

Maps TCR data to an existing reference clonotype table using similarity matrices at a specified stringency level. Useful for mapping new data against previously identified clonotypes.

Usage

assign_clonotype_from_reference(
  TCR_data,
  ref_table,
  similarity_matrix_type = .mapping.levels,
  clone_definition_df = .clone.definition.df
)

Arguments

TCR_data: A data frame with columns Sample, TRA_1, TRA_2, TRB_1, TRB_2.
ref_table: A reference table with columns Sample, TRA_1, TRA_2, TRB_1, TRB_2, and CloneID (as output by identify_clonotypes).
similarity_matrix_type: Which stringency level to use for matching. One of the values in .mapping.levels.
clone_definition_df: Clone definition data frame.

Value

A character vector of mapped clone IDs, with NA for unmapped cells and pipe-separated IDs for cells matching multiple clonotypes.