0.16.6 documentation

Complete canonical API text; task articles explain the workflows. Tutorials

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Setup and learning paths

HomeInstall and prepare the environmentChoose your learning module

Module I · Chord

1.1 Tables and field meanings1.2 Produce and import comparisons1.3 Build the layers step by step1.4 Direction, curvature and clearance1.5 Filter and summarize links1.6 Full source-file workflow1.7 Complete chord showcase

Module II · Collinear

2.1 Reuse chord input tables2.2 Switch coordinates and add layers2.3 Routes, clearance and the ruler2.4 Compare CDS neighbourhoods2.5 Focus, anchors and segments2.6 Complete collinear showcase

Module III · Plasmid

3.1 DNA, annotations and 13 references3.2 From a circle to annotation layers3.3 Features, primers and restriction3.4 Thirteen plasmid references3.5 Complete plasmid cases

Consult as needed · Data and layers

Prepare tables and coordinatesImport and convert dataImport nucleotide and protein alignmentsProject protein intervals to genomic coordinatesFeatures, stacking and genomic decorationLabels and local placementQuantitative tracksMappings, scales, guides and themesSet values by sequence and strandCommon adjustments and grammarExport, preview and diagnostics

Learning map and reference

Articles and complete workflowsFunction referenceReproducible galleryFrequently asked questionsMigrate to the candidate APITerminology and design sourcesDevelopment status and changes

Filter restriction sites for display

On this page

• Usage
• Arguments
• Value
• See also
• Examples

Filter restriction sites for display

Usage

Code

filter_restriction_sites(
  sites,
  set = c("all", "unique", "unique_dual", "six_plus", "unique_6plus", "commercial",
    "reference"),
  enzymes = NULL,
  min_site_length = NULL,
  cuts = NULL,
  window = NULL,
  commercial_only = FALSE,
  parent_set = c("all", "commercial_all", "commercial_nonredundant")
)

Arguments

sites

Result from find_restriction_sites().

set

Display preset. "reference" reuses the enzyme-set profile stored for an exactly recognized reference sequence. It errors when no such profile is available. A saved "None" profile returns no sites.

enzymes, min_site_length, cuts, window, commercial_only

Additional filters.

parent_set

Enzyme catalogue subset. "commercial_nonredundant" keeps one stable commercial representative per equivalent recognition group and site, preferring the database's preferred enzyme when present.

Value

A row subset whose biological coordinates are unchanged.

See also

ggchord_data_contract

Examples

Code

data(plasmid_example_pSpCas9_BB_2A_GFP_PX458)
sites <- find_restriction_sites(
  plasmid_example_pSpCas9_BB_2A_GFP_PX458
)
reference_sites <- filter_restriction_sites(sites, set = "reference")