getDiamondInsulation: Contact map insulation
In js2264/cooleR: Analysing cool files in R with HiContacts

getDiamondInsulation

R Documentation

Contact map insulation

Description

Computes diamond insulation score along the entire genome

Usage

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)
diams <- getDiamondInsulation(hic)
getDiamondInsulation(diams)

js2264/cooleR documentation built on Jan. 29, 2024, 10:47 p.m.