Contact map insulation

Computes diamond insulation score along the entire genome

getDiamondInsulation(x, window_size = NULL, BPPARAM = BiocParallel::bpparam())

getBorders(x, weak_threshold = 0.2, strong_threshold = 0.5)

Arguments

x

A HiCExperiment object over a full genome

window_size

Which window size to use to compute diamond insulation score (default: 10 * resolution)

BPPARAM

BiocParallel parallelization settings

weak_threshold

Less stringent cutoff to call borders in the diamond insulation score

strong_threshold

More stringent cutoff to call borders in the diamond insulation score

Value

a HiCExperiment object with additional insulation metadata, containing the diamond insulation score computed

Examples

library(HiContacts)
hic <- contacts_yeast() |> 
  refocus('II:1-300000') |> 
  zoom(1000)
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
diams <- getDiamondInsulation(hic)
#> Going through preflight checklist...
#> Scan each window and compute diamond insulation score...
#> Annotating diamond score prominence for each window...
getDiamondInsulation(diams)
#> Going through preflight checklist...
#> Scan each window and compute diamond insulation score...
#> Annotating diamond score prominence for each window...
#> `HiCExperiment` object with 146,812 contacts over 300 regions 
#> -------
#> fileName: "/github/home/.cache/R/ExperimentHub/11307d784c99_7752" 
#> focus: "II:1-300,000" 
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 1000 
#> interactions: 18286 
#> scores(2): count balanced 
#> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0) centromeres(16) 
#> pairsFile: N/A 
#> metadata(1): insulation