select.primers.by.cvg: Greedy Optimization.
In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

select.primers.by.cvg

R Documentation

Greedy Optimization.

Description

Greedy approach for solving the primer set coverage problem.

Usage

select.primers.by.cvg(
  primers,
  settings,
  template.df,
  mode.directionality = c("fw", "rev"),
  required.cvg = 1,
  allowed.mismatches,
  primer_conc,
  na_salt_conc,
  mg_salt_conc,
  k_salt_conc,
  tris_salt_conc,
  template_conc,
  allowed.other.binding.ratio,
  allowed.stop.codons,
  allowed.region.definition = c("within", "any"),
  disallowed.mismatch.pos,
  target.temps = NULL,
  fw.primers = NULL,
  updateProgress = NULL
)

Arguments

`primers`	Primer data frame to be optimized.
`settings`	A `DesignSettings` object.
`template.df`	Template data frame.
`mode.directionality`	Primer direction.
`required.cvg`	Target coverage ratio.
`allowed.mismatches`	The number of mismatches primers are allowed to have with the templates.
`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.
`template_conc`	Template data frame.
`allowed.other.binding.ratio`	Ratio of primers allowed to bind to non-target regions.
`allowed.stop.codons`	Consider mismatch binding events that induce stop codons.
`allowed.region.definition`	Definition of the target binding sites used for evaluating the coverage. If `allowed.region.definition` is `within`, primers have to lie within the allowed binding region. If `allowed.region.definition` is `any`, primers have to overlap with the allowed binding region. The default is that primers have to bind within the target binding region.
`disallowed.mismatch.pos`	The number of positions from the primer 3' end where mismatches should not be allowed. All primers binding templates with mismatches within `disallowed.mismatch.pos` from the 3' end are disregarded.
`target.temps`	Target melting temperatures for optimized sets in Celsius.
`fw.primers`	List with already optimized primer data frames corresponding to `target.temps`.
`updateProgress`	Shiny progress callback function.