generate_cost_matrix: Generate a simple cost matrix

In seqtrie: Radix Tree and Trie-Based String Distances

Generate a simple cost matrix

Description

Generate a cost matrix for use with the search method.

Usage

generate_cost_matrix(charset, ambiguity_base = NULL, match = 0L, mismatch = 1L)

Arguments

charset	A string of all allowed characters in both query and target sequences (e.g. "ACGT").
ambiguity_base	A single character (e.g. "N") that will match any character in charset at the cost of match. Defaults to NULL.
match	Integer cost of a match.
mismatch	Integer cost of a mismatch.

Value

A square cost matrix with row- and column-names given by charset, plus the optional ambiguity_base. Gap costs are no longer included here; pass gap_cost and gap_open_cost to distance/search functions.

Examples

generate_cost_matrix("ACGT", match = 0, mismatch = 1)
generate_cost_matrix("ACGT", ambiguity_base = "N", match = 0, mismatch = 1)

seqtrie documentation built on Nov. 5, 2025, 7:43 p.m.