Calculates the p-epitope antigenic distance between two aligned amino acid sequences of influenza HA using epitope residue sites defined for the specified subtype. Several summary modes are supported, including the dominant (maximum), mean, median, and Anderson's average definition.
Usage
pepitope(
seq_1,
seq_2,
subtype,
mode = "dominant",
harmonize_b_lineages = TRUE,
ambiguous_residues = "xX?"
)Arguments
- seq_1, seq_2
Character strings. Aligned amino acid sequences.
- subtype
Character. HA subtype or lineage (e.g., `"H1N1"`, `"H3N2"`, `"B/Victoria"`).
- mode
Character. Summary mode to apply across epitope sites. Options: `"dominant"` (default), `"mean"`, `"median"`, `"anderson"`, or `epitope` to return per-epitope distances.
- harmonize_b_lineages
Logical. Whether to treat B lineages as unified. Defaults to `TRUE`.
- ambiguous_residues
Optional argument (currently unused).