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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

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Find genomic loci around explicitly identified features

On this page

• Usage
• Arguments
• Value
• Details
• See also
• Examples

Selects targets by feature_id and expands their genomic bounds using biological upstream/downstream directions. For a negative-strand target, upstream extends towards larger genomic coordinates. Unknown or bidirectional strands require equal upstream and downstream distances. Windows are clipped to the known full sequence length; clipping is reported.

Usage

Code

find_ggchord_loci(
  seq_data,
  feature_data,
  targets,
  upstream = 0,
  downstream = 0
)

Arguments

seq_data

Sequence table containing unique accver and positive integer length values. Optional genome and genome_id columns are retained in the returned windows.

feature_data

Feature table containing feature_id, accver, start, end, and optionally strand. Missing strand means unknown.

targets

Non-empty character vector of distinct feature_id values. Selection is exact; no annotation text or accession versions are guessed.

upstream, downstream

Single non-negative integer numbers of bases added before and after each target in its biological direction.

Value

An ordinary data frame in target order with target_id, locus_id, accver, start, end, strand, unexpanded target_start and target_end, requested extensions, and clipped_left/clipped_right. The target_source_rows list column identifies feature input rows used for each target. Coordinates refer to the supplied sequence table; no implicit change from focused coordinates to an earlier source is made.

Details

Repeated rows with the same feature_id represent segments of one target and must belong to the same sequence and strand. Their outer bounds define the target window. Different targets always produce separate windows, including overlapping targets on the same sequence. No intervening sequence is removed, concatenated or locally reversed. Ordered one-based inclusive genomic coordinates are required; origin-spanning circular features and protein coordinates need an explicit conversion before this operation.

The returned locus_id equals target_id. Pass the returned table as loci to focus_ggchord_data() to create independent focused sequences named by those IDs, including multiple windows from one source sequence.

See also

ggchord_data_contract

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
data(gene_data_example)
genes <- gene_data_example |>
  transmute(accver, start, end, strand = source_strand)
genes <- genes |>
  mutate(feature_id = paste(accver, start, end, sep = ":"))
find_ggchord_loci(seqs, genes, targets = genes$feature_id[1], upstream = 100, downstream = 100)