cascaded.filter: Filtering for the Optimization

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Filtering for the Optimization

Description

Filter primers according to constraints and relax constraints if necessary.

Usage

cascaded.filter(
  primer.df,
  template.df,
  settings,
  mode.directionality = c("fw", "rev", "both"),
  required.cvg = 1,
  target.temps = NULL,
  updateProgress = NULL,
  results.loc = NULL
)

Arguments

primer.df	Primer data frame.
template.df	Template data frame.
settings	Settings object.
mode.directionality	Primer direction.
required.cvg	Required ratio of covered templates. If required.cvg is set to 0, the constraints are not relaxed.
target.temps	Target melting temperature of the primers in Celsius. This argument is only required if we try to match the melting temperatures of another primer set, e.g. when first optimizing forward and then optimizing reverse primers.
updateProgress	Progress callback function for shiny.
results.loc	Directory where the filtering results should be stored.

Details

Constraints are relaxed if the required.cvg could not be reached with the input constraints.

Value

The filtered primer data frame with respect to required.cvg.

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