get_covered.vanilla: Determination of the Covered Sequences.
In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

get_covered.vanilla

R Documentation

Determination of the Covered Sequences.

Description

Determines the covered template sequences given by template.df that are covered by the primers given by primers.

Usage

get_covered.vanilla(primers, template.df, mode.directionality = NULL)

Arguments

`primers`	A `Primers` object containing the primers for which the coverage should be evaluated.
`template.df`	A `Templates` object containing the template sequences corresponding to `primers`.
`mode.directionality`	If `mode.directionality` is provided, the coverage of templates is computed for a specific direction of primers. Either "fw" (forward coverage only), "rev" (reverse coverage only), or "both" for both directions. If `mode.directionality` is not provided the direction is determined by the input primers.

Details

The manner in which the coverage ratio is evaluated depends on the directionality of the input primers. If either only forward or reverse primers are inputted, the individual coverage of each primer is used to determine the overall coverage. If, however, forward and reverse primers are inputted at the same time, the coverage is defined by the intersection of binding events from both, forward and reverse primers.