Retrieve the BSD4 substitution matrix

Returns the BSD4 (BLOSUM-derived substitution distance 4) matrix used internally for amino acid distance scoring in TCRdist calculations. The matrix is built in C++ and returned as a named numeric matrix in R.

Usage

bsd4_matrix()

Value

A named numeric matrix of amino acid substitution distances. Row and column names are the 20 standard single-letter amino acid codes in AMINO_ACIDS order.

See also

weighted_cdr3_distance, AMINO_ACIDS

Examples

# \donttest{
bsd4 <- bsd4_matrix()
bsd4["A", "A"]  # 0
#> [1] 0
bsd4["A", "G"]  # small positive value
#> [1] 4
# }