compute.constraints: Computation of Constraints.

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Computation of Constraints.

Description

Computes the specified constraints for the input primers.

Usage

compute.constraints(
  primer.df,
  mode.directionality = c("fw", "rev", "both"),
  template.df,
  settings,
  active.constraints = c("primer_coverage", "primer_length", "primer_specificity",
    "gc_clamp", "gc_ratio", "no_runs", "no_repeats", "self_dimerization",
    "cross_dimerization", "melting_temp_range", "melting_temp_diff",
    "secondary_structure", "primer_efficiency", "annealing_DeltaG", "stop_codon",
    "terminal_mismatch_pos", "substitution", "hexamer_coverage", "coverage_model",
    "off_primer_efficiency", "off_annealing_DeltaG", "off_coverage_model"),
  no.structures = FALSE,
  for.shiny = FALSE,
  updateProgress = NULL
)

Arguments

primer.df	Primer data frame.
mode.directionality	Primer directionality.
template.df	Template data frame.
settings	A DesignSettings object.
active.constraints	Strings giving the constraints that are to be computed.
no.structures	Whether dimer structures shall be computed.
for.shiny	Whether to format output for HTML.
updateProgress	Progress callback function for shiny.

Value

A data frame with columns for each constraint in active.constraints.

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