optimize.primer.cvg: Greedy Optimization

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Greedy Optimization

Description

Greedy approach for solving the primer set coverage problem.

Usage

optimize.primer.cvg(
  primers,
  template.df,
  mode.directionality,
  cur.opti.constraints,
  target.temp,
  allowed.mismatches,
  opti.limits,
  primer_conc,
  na_salt_conc,
  mg_salt_conc,
  k_salt_conc,
  tris_salt_conc,
  updateProgress = NULL
)

Arguments

primers	Primer data frame to be optimized.
template.df	Template data frame.
mode.directionality	Primer direction.
cur.opti.constraints	List with optimization constraint settings.
target.temp	Target annealing temperature of the optimized primer set in Celsius.
allowed.mismatches	The number of mismatches primers are allowed to have with the templates.
opti.limits	List with optimization limits.
primer_conc	Primer concentration.
na_salt_conc	Sodium ion concentration.
mg_salt_conc	Magensium ion concentration.
k_salt_conc	Potassium ion concentration.
tris_salt_conc	Tris ion concentration.
updateProgress	Shiny progress callback function.
template_conc	Template concentration.

Value

List with optimization data.

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