Get the substitution matrix.

Source: R/get_substitution_mtx.R

Get the substitution matrix.

get_substitute_mtx(mtx.name = "BLOSUM62", gap.char = "-",
  gap.gap = NA, gap.non.gap = NA)

Arguments

mtx.name

A character string. The name of substitution matrix. Available choices are "BLOSUM45", "BLOSUM50", "BLOSUM62", "BLOSUM80", "BLOSUM100", "PAM30", "PAM40", "PAM70", "PAM120", "PAM250".
gap.char

A character for gap. Default is "-".
gap.gap

A numeric value. Custom score for gap vs gap that overrides the default in the substitution matrix. Do not override if set to NA.
gap.non.gap

A numeric value. Custom score for gap vs gap that overrides the default in the substitution matrix. Do not override if set to NA.

Value

A substitution matrix.

Examples

# NOT RUN {
get_substitution_mtx("BLOSUM62", gap.char="*")
# }