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Create a ChromatinContacts object

Source: R/AllClasses.R
ChromatinContacts.Rd

Constructor for ChromatinContacts from cooler files (.cool or .mcool).

Usage

ChromatinContacts(cooler_path, focus = NULL, resolution = NULL)

Arguments

cooler_path

Character. Path to .cool or .mcool file.

focus

Character, GInteractions, or NULL. Genomic region(s) to focus:

  • Single region: "chr1" or "chr1:1-1000000"

  • Inter-chromosomal: "chr1&chr2" (excludes diagonal)

  • All combinations: "chr1|chr2" (includes intra-chromosomal)

  • Multiple: c("chr1&chr2", "chr3|chr4")

  • NULL for genome-wide (default)

resolution

Integer. Resolution in base pairs (required for .mcool).

Value

A ChromatinContacts object.

See also

import-ChromatinContacts, resolution(), focus(), features()

Examples

if (FALSE) { # \dontrun{
# Genome-wide .cool file
cc <- ChromatinContacts("file.cool")

# Multi-resolution .mcool
cc <- ChromatinContacts("file.mcool", resolution = 5000L)

# Focus on chromosome
cc <- ChromatinContacts("file.cool", focus = "chr1")

# Inter-chromosomal between chr1 and chr2
cc <- ChromatinContacts("file.cool", focus = "chr1&chr2")
} # }