# In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis



out.df <- openPrimeR:::view.primers.report(params$primers, params$templates)
#"$\\Delta \\text{T}_\\text{m}$")
knitr::kable(out.df, row.names = FALSE, caption = "Overview of the analyzed primers. If forward and reverse primers are present, primers are paired such as to maximize the coverage. Ambiguous bases are shown in italics. The \\textit{Coverage} column indicates the percentage of template sequences that are covered by each primer. \\textit{Mismatches} gives the percentage of coverage events that are subject to a certain number of mismatches. \\textit{Position} indicates the major binding mode of a primer relative to the end of the target binding region. Negative values indicate binding upstream of the specified region, while positive positions indicate binding downstream of the target region.",
escape = TRUE, longtable = TRUE)


# Coverage

cvg.stats <- openPrimeR::get_cvg_stats(params$primers, params$templates)

out.stats <- openPrimeR::get_cvg_stats(params$primers, params$templates, for.viewing = TRUE)
knitr::kable(out.stats, row.names = FALSE, caption = "Number of covered template sequences per group. In case that primers for both directions are present, the \\textit{Coverage (fw)} and \\textit{Coverage (rev)} columns refer to the individual coverage of forward and reverse primers, respectively. If primers of both directions are present, the total coverage is determined by the intersection of coverage events from primers of both directions. If, however, only primers of a single direction are present, the coverage solely depends on the primers of the given direction.", longtable = TRUE)


r refers to the number of template sequences for which fully complementary primers exist. \textit{Expected Coverage} indicates the expected number of covered templates, which is determined by applying the coverage constraints to the set of potential coverage events for the specified number of maximal mismatches. \textit{Available Templates} shows the total number of available template sequences per group."} openPrimeR::plot_template_cvg(params$primers, params$templates)

r refers to the fact that the subsets were selected such as to maximize the coverage. The line plot indicates the total percentage of covered template sequences, while the bars indicate the percentage of covered templates for individual primers. The cumulative coverage of the bars can exceed 100 percent because different primers may cover the same template redundantly. The target coverage ratio is indicated by the dashed horizontal line.'}
primer.subsets <- openPrimeR::subset_primer_set(params$primers, params$templates)
openPrimeR::plot_primer_subsets(primer.subsets, params$templates, required.cvg = params$required_cvg)


r indicates the region where the forward primers should bind, while \textit{Amplification region} indicates the following region.'} if (params$direction == "fw" || params$direction == "both") { openPrimeR::plot_primer_binding_regions(params$primers, params$templates, relation = "fw") }

# Physicochemical properties

r
openPrimeR::plot_constraint_fulfillment(params$primers, params$settings)

openPrimeR::plot_constraint_deviation(params$primers, params$settings)



# reset theme to previous setting
ggplot2::theme_set(old.theme)


matdoering/openPrimeR documentation built on Feb. 10, 2020, 4:16 p.m.