compute.primer.efficiencies: Primer Efficiency.

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Primer Efficiency.

Description

Computes the efficiency of primer binding events for Taq polymerase.

Usage

compute.primer.efficiencies(
  primer.df,
  template.df,
  annealing.temp,
  taqEfficiency,
  primer_conc,
  na_salt_conc,
  mg_salt_conc,
  k_salt_conc,
  tris_salt_conc,
  mode = c("on_target", "off_target")
)

Arguments

primer.df	Primer data frame.
template.df	Template data frame.
annealing.temp	Annealing temperature for which to evaluate efficiency.
taqEfficiency	Whether the efficiency shall be computed using a mismatch-model developed for Taq polymerases. The default setting is TRUE. Set taqEfficiency to FALSE if you are using another polymerase than Taq.
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.
mode	Compute efficiencies for on-target coverage events (on_target) or off-target coverage events (off_target).

Details

This function uses DECIPHER's CalculateEfficiencyPCR.

Value

A list with the efficiency of every primer binding event.

Examples

data(Ippolito)
p <- PCR(settings)
# Requires OligoArrayAux software:
## Not run: 
eff.df <- compute.primer.efficiencies(primer.df, template.df, 55, 
             p$primer_concentration, p$Na_concentration,
             p$Mg_concentration, p$K_concentration, p$Tris_concentration)

## End(Not run) 

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