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)
A HiCExperiment
object over a full genome
Which window size to use to compute diamond insulation score (default: 10 * resolution)
BiocParallel parallelization settings
Less stringent cutoff to call borders in the diamond insulation score
More stringent cutoff to call borders in the diamond insulation score
a HiCExperiment
object with additional insulation
metadata,
containing the diamond insulation score computed
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