openPrimeR-package {openPrimeR} | R Documentation

## Multiplex PCR Primer Design and Analysis.

### Description

With openPrimeR you can evaluate existing primers or design novel primers for multiplex polymerase chain reaction that are optimized with respect to the coverage of template sequences and the physicochemical properties of the primers.

### Details

For designing primers, you just need the function `design_primers` from openPrimeR. As a minimal input, this function requires:

A set of template sequences

  You an load a `Templates` object with `read_templates`.

Settings for primer design

  You can load a `DesignSettings` object from a (supplied) XML file with `read_settings`. The settings can be easily customized using the setters `constraints`, `constraintLimits`, `cvg_constraints`, `conOptions`, and `PCR`.

For evaluating existing primers you can load a FASTA or CSV file containing the primers and templates of of interest using `read_primers` and `read_templates`, respectively. After evaluating the properties of the primers using `check_constraints`, you can interpret the results with several functions. For example, you can analyze the coverage of the template sequences using `get_cvg_stats`, determine the deviation from the target constraints using `plot_constraint_deviation`, or create a comprehensive report on the analyzed primers using `create_report`. In order to compare several primer sets with each other, you can create a table of the properties of the primer sets using `get_comparison_table` or create a full report, again using `create_report`.

### Package options

openPrimeR uses the following options:

`openPrimeR.constraint_order`

  The identifiers of constraints in the order they are applied during the filtering procedure. This order is maintained when loading a `DesignSettings` object.

`openPrimeR.relax_order`

  The identifiers of constraints in the order in which they shall be relaxed during the relaxation procedure when designing primers.

`openPrimeR.plot_abbrev`

  The maximal number of allowed characters for tick labels in plots.

`openPrimeR.plot_colors`

  A named vector providing the identifiers of RColorBrewer palettes. Each vector entry provides the plotting colors for a specific type of stratification (i.e. by run, constraint, or primer). The palettes should provide at least eight colors.

### Author(s)

Maintainer: Matthias Döring mdoering@mpi-inf.mpg.de

Authors:

- Nico Pfeifer pfeifer@informatik.uni-tuebingen.de

[Package openPrimeR version 1.8.0 Index]