Map clonotypes from allele format to paired TCR format — map_clonotypes_to_paired

Maps TCR data from individual allele format (TRA_1/TRA_2/TRB_1/TRB_2) to paired alpha/beta chain format (TRA/TRB). Useful when the reference table uses only TRA and TRB (no second allele) and you want to map allele-level data to this paired format.

Usage

map_clonotypes_to_paired_TCR(
  data_to_map,
  ref_table,
  col_to_map,
  map_to_label = NULL
)

Arguments

data_to_map: A data frame with columns Sample, TRA_1, TRA_2, TRB_1, TRB_2.
ref_table: A reference table with columns Sample, TRA, TRB, and the column specified by col_to_map.
col_to_map: Name of the column in ref_table to map values from.
map_to_label: Optional data frame for additional label mapping. Row names should correspond to mapped values. Factor and non-factor columns are handled differently.

Value

A data frame with mapping results including strict and loose matches, mapping type (strict/loose_A/loose_B/ND), and optionally label-mapped columns.