design_primers.single: Design Primers for a Single Direction
In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

design_primers.single

R Documentation

Design Primers for a Single Direction

Description

Designs primers for a single direction.

Usage

design_primers.single(
  template.df,
  sample.name,
  mode.directionality = c("fw", "rev"),
  settings,
  timeout,
  opti.algo,
  allowed.region.definition,
  init.algo,
  max.degen,
  conservation,
  target.temps,
  required.cvg,
  fw.primers = NULL,
  cur.results.loc = NULL,
  primer.df = NULL,
  updateProgress = NULL
)

Arguments

`template.df`	Template data frame with sequences for which primers shall be designed.
`sample.name`	Identifier for the templates.
`mode.directionality`	Template strands for which primers shall be designed. Primers can be designed either only for forward strands, only for reverse strands, or both strand directions.
`settings`	A `DesignSettings` object specifying the criteria for designing primers.
`timeout`	Timeout in seconds for the optimization with ILPs.
`opti.algo`	The algorithm to be used for solving the primer set covering problem.
`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.
`init.algo`	The algorithm to be used for initializing primers. If `init.algo` is `naive`, then primers are constructed from substrings of the input template sequences. If `init.algo` is `tree`, phylogenetic trees are used to form degenerate primers whose degeneracy is bounded by `max.degen`.
`max.degen`	Maximal degeneracy of merged primers.
`conservation`	When using the tree-based primer initialization, consider only the `conservation` percentile of regions with the highest conservation.
`target.temps`	Target melting temperatures for optimized primer sets in Celsius. Only required when optimizing primers for both strand directions and one optimization was already performed.
`required.cvg`	The target ratio of covered template sequences. If the target ratio cannot be reached, the constraint settings are relaxed up to the relaxation limits.
`fw.primers`	List with optimized primer data frames corresponding to `target.temps`. Only required for optimizing both strand directions and only in the second optimization run in order to check for cross dimerization.
`cur.results.loc`	Directory for storing results of the primer design procedure.
`primer.df`	A data frame of evaluated primer candidates that can be optimized directly.
`updateProgress`	Shiny progress callback function.

Value

A list containing the results of the primer design procedure:

opti:: A Primers object representing the set of optimized primers.
all_results:: A list containing the optimal results for each sampled melting temperature range in terms of a Primers object in case that the melting_temp_diff constraint was active. Otherwise, all_results only has a single entry representing a primer set relating to an undefined melting temperature.
used_constraints:: A DesignSettings object with the (adjusted) analysis settings.
filtered:: A Primers object containing the primer candidates that passed the filtering procedure and which gave rise to the final optimal set.