compute.basic.details: Computation of Coverage Details

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Computation of Coverage Details

Description

Determines binding properties of primers.

Usage

compute.basic.details(
  binding,
  mode = c("on_target", "off_target"),
  template.df,
  primers,
  mode.directionality = c("fw", "rev", "both"),
  allowed.mismatches,
  allowed.other.binding.ratio,
  allowed.region.definition = c("within", "any"),
  updateProgress = NULL
)

Arguments

binding	An IRanges object with primer binding information.
mode	Either on_target for on-target binding or off_target for off-target binding.
template.df	Template data frame.
primers	Primer data frame.
mode.directionality	Primer directionality.
allowed.mismatches	The number of allowed mismatches per binding event.
allowed.other.binding.ratio	Ratio of primers that are allowed to bind to non-allowed regions. If allowed.other.binding.ratio >0 primers are allowed to bind at any location within the templates. However, a warning is given if the ratio of primers binding to non-target regions exceeds the allowed.other.binding.ratio.
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.
updateProgress	Progress callback function for shiny.

Value

Primer data frame with information on the covered template sequences.

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