compute.efficiency: 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.efficiency(
  fw.primers,
  fw.start,
  fw.end,
  covered,
  taqEfficiency,
  annealing.temp,
  primer_conc,
  sodium.eq.concentration,
  mode.directionality = c("fw", "rev"),
  seqs
)

Arguments

fw.primers	Primer sequence strings.
fw.start	Binding position (start).
fw.end	Binding position (end).
covered	List of covered template indices per primer.
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.
annealing.temp	Annealing temperature for which to evaluate efficiency.
primer_conc	Primer concentration.
sodium.eq.concentration	The sodium-equivalent concentration of ions.
mode.directionality	Primer directionality.
seqs	Template sequence strings.

Details

This function uses DECIPHER's CalculateEfficiencyPCR.

Value

The efficiencies of primer binding events.

References

Wright, Erik S., et al. "Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates." Environmental microbiology 16.5 (2014): 1354-1365.

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