check.mutations: Identification of Mismatch Mutations.

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Identification of Mismatch Mutations.

Description

Identifies primers that induce mutations due to mismatch binding.

Usage

check.mutations(
  primer.seq,
  pos.start,
  pos.end,
  template.df,
  covered.seqs,
  ORF.data,
  mode.directionality = c("fw", "rev"),
  mutation.types = c("stop_codon", "substitution")
)

Arguments

primer.seq	Primer sequence string.
pos.start	Binding position of primer (start).
pos.end	Binding position of primer (end).
template.df	Template data frame.
covered.seqs	Identifiers of covered templates.
ORF.data	Reading frame information of templates.
mode.directionality	Directionality of primers.
mutation.types	Character vector of the mutation types to be checked for.

Details

Checks for one primer and all covered templates whether any templates are bound with mismatches such that a forbidden mutation is induced. A boolean vector indicating which binding events induce a forbidden mutation is returned.

Value

TRUE if the primer.seq induces a mutation that is forbidden according to the provided mutation.types.

matdoering/openPrimeR documentation built on July 4, 2025, 3:59 a.m.