Contacts: Contacts

In js2264/cooleR: Analysing cool files in R with HiContacts

Contacts

Description

This function has been deprecated in favor of the generic HiCExperiment() constructor (from HiCExperiment package).

Usage

Contacts(
  file,
  resolution = NULL,
  focus = NULL,
  metadata = list(),
  topologicalFeatures = S4Vectors::SimpleList(loops =
    S4Vectors::Pairs(GenomicRanges::GRanges(), GenomicRanges::GRanges()), borders =
    GenomicRanges::GRanges(), compartments = GenomicRanges::GRanges(), viewpoints =
    GenomicRanges::GRanges()),
  pairsFile = NULL
)

Arguments

file	Path to a (m)cool file
resolution	Resolution to use with mcool file
focus	focus Chr. coordinates for which interaction counts are extracted from the .(m)cool file, provided as a character string (e.g. "II:4001-5000"). If not provided, the entire (m)cool file will be imported.
metadata	list of metadata
topologicalFeatures	topologicalFeatures provided as a named SimpleList
pairsFile	Path to an associated .pairs file

Value

a new HiCExperiment object.

Examples

library(HiContacts)
library(HiContactsData)
mcool_path <- HiContactsData::HiContactsData('yeast_wt', 'mcool')
Contacts(mcool_path, resolution = 1000)

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