get_cvg_stats-list-method: Coverage Statistics for Multiple Primer Sets.

get_cvg_stats,list-methodR Documentation

Coverage Statistics for Multiple Primer Sets.

Description

Retrieve statistics on covered templates for multiple primer sets.

Usage

## S4 method for signature 'list'
get_cvg_stats(
  primers,
  templates,
  for.viewing = FALSE,
  total.percentages = FALSE,
  allowed.mismatches = Inf,
  cvg.definition = c("constrained", "basic")
)

Arguments

primers

A list with objects of class Primers containing primers with evaluated coverage.

templates

A list with objects of class Templates containing templates with evaluated coverage.

for.viewing

Whether the table should be formatted for viewing rather than processing.

total.percentages

Whether group coverage percentages should relate to all template sequences or just those templates belonging to a specific group.

allowed.mismatches

The maximal allowed number of mismatches. By default, the number of mismatches is not restricted.

cvg.definition

If cvg.definition is set to "constrained", the statistics for the expected coverage (after applying the coverage constraints) are retrieved. If cvg.definition is set to "basic", the coverage is determined solely by string matching (i.e. without applying the coverage constraints). By default, cvg.definition is set to "constrained".

Value

Data frame with coverage statistics.


matdoering/openPrimeR documentation built on Feb. 11, 2024, 9:22 p.m.