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Weighted CDR3 distance between two CDR3 sequences

Source: R/wrappers_distance.R
weighted_cdr3_distance.Rd

Computes the TCRdist CDR3 component distance between two amino acid CDR3 sequences. Accounts for length differences via gap penalties and uses BSD4 substitution scores on the aligned positions. Dispatches to a C++ implementation for performance.

Usage

weighted_cdr3_distance(
  seq1,
  seq2,
  weight = WEIGHT_CDR3_REGION,
  gap_penalty = GAP_PENALTY_CDR3_REGION
)

Arguments

seq1

Character string of length 1. First CDR3 amino acid sequence. Must be non-empty.

seq2

Character string of length 1. Second CDR3 amino acid sequence. Must be non-empty.

weight

Integer. Weight applied to the alignment score component. Defaults to WEIGHT_CDR3_REGION (3L).

gap_penalty

Integer. Penalty per gap character in length differences. Defaults to GAP_PENALTY_CDR3_REGION (12L).

Value

A numeric scalar: the weighted CDR3 distance.

See also

tcrdist_matrix, bsd4_matrix

Examples

# \donttest{
weighted_cdr3_distance("CASSIRSSYEQYF", "CASSIRSYEQYF")
#> [1] 12
weighted_cdr3_distance("CASSIRSSYEQYF", "CASSIRSSYEQYF")  # 0
#> [1] 0
# }