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Summarise genomic context around genome-scan signals

Source: R/genome_scan_context.R
genome_scan_context.Rd

A regional peak is easier to interpret when the analyst can ask whether it overlaps low recombination, unusual marker density, increased missingness, a sequencing or mapping batch, a candidate inversion, or a signal supported by a method based on a different genomic signature.

Use this function after basic quality control but before interpreting genome scans. When candidate inversion regions exist, compare at least three views: the complete genome, a collinear sensitivity analysis excluding candidate regions, and an inversion-specific analysis. Candidate regions are annotated but never silently excluded.

Usage

genome_scan_context(
  data,
  window.snps = 250L,
  step.snps = window.snps,
  window.bp = NULL,
  step.bp = window.bp,
  inversion.regions = NULL,
  scan.statistics = NULL,
  ld.max.snps = 250L,
  filename = "genome_scan_context",
  verbose = TRUE,
  ...
)

Arguments

data

A GDS filepath or open SeqVarGDSClass object.

window.snps

Number of SNPs per fixed-SNP window. Default: window.snps = 250.

step.snps

Number of SNPs between window starts. Default: step.snps = window.snps.

window.bp

Optional physical window size in base pairs. Supplying it replaces fixed-SNP windows. Default: window.bp = NULL.

step.bp

Physical distance between window starts. Default: step.bp = window.bp.

inversion.regions

Optional table, or the result from detect_inversions(). A table requires chromosome, start, and end; candidate_id and candidate_class are retained when present. Default: inversion.regions = NULL.

scan.statistics

Optional marker-level table with chromosome, position, and one or more scan statistics. Column names are matched without regard to case. Numeric statistics are summarised by window mean, median, and maximum. Default: scan.statistics = NULL.

ld.max.snps

Maximum evenly spaced SNPs used for LD in each window. Default: ld.max.snps = 250.

filename

Output filename stem. Default: filename = "genome_scan_context".

verbose

Logical. Display progress messages. Default: verbose = TRUE.

...

Standard radr workflow arguments, including path.folder.

Value

A list containing the window context table, normalised region table, plots, data-source information, and output paths.

Details

Build a window-level context table for interpreting regional genome-scan peaks. The table places marker density, call rate, heterozygosity, minor allele frequency, depth when available, local LD, candidate inversion or structural-region annotations, and user-supplied scan statistics beside one another. It does not decide whether a region is under selection.

The context table is descriptive. Overlap with an inversion-like haploblock, centromere, low-recombination region, assembly gap, or technical anomaly changes the interpretation of a peak but does not by itself validate or invalidate selection. Repeat analyses after excluding putative heterokaryotypes when arrangement calls are available, and seek support from methods based on different summaries.

References

Booker TR, Yeaman S, Whitlock MC (2020). Variation in recombination rate affects detection of outliers in genome scans under neutrality. Molecular Ecology, 29, 4274-4279.

Faria R, Johannesson K, Butlin RK, Westram AM (2019). Evolving inversions. Trends in Ecology & Evolution, 34, 239-248.