Skip to contents

ChromatinContacts S4 class

Source: R/AllClasses.R
ChromatinContacts-class.Rd

S4 class representing chromatin contact data from cooler files (.cool or .mcool). Memory-efficient pointer that loads data only when import() is called.

Details

Key features:

  • Memory-efficient: loads data only when needed

  • Flexible focusing: subset regions before or after import

  • Feature integration: automatically subsets attached features

  • Multi-resolution: supports both .cool and .mcool files

Focus parameter options:

  • Single region: "chr1:1000000-2000000"

  • Whole chromosome: "chr1"

  • Multiple regions (all combinations): "chr1 | chr2"

  • Inter-chromosomal only: "chr1 & chr2"

  • GInteractions object for programmatic control

Slots

cooler_path

Character. Path to cooler file.

resolution

Integer or NULL. Resolution in base pairs (required for .mcool files).

focus

GInteractions or NULL. Genomic regions of interest (NULL for genome-wide).

interactions

GInteractions or NULL. Imported Hi-C interaction data.

seqinfo

Seqinfo or NULL. Genome assembly sequence information.

compartments

GRanges or NULL. A/B compartment annotations.

TADs

GRanges or NULL. Topologically associating domains.

loops

GInteractions or NULL. Chromatin loop calls.

multi_contacts

GRanges or NULL. Multi-way contact regions.

tracks

GRangesList. Genomic signal tracks (ChIP-seq, ATAC-seq, etc.).

See also

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

Examples

if (FALSE) { # \dontrun{
# Create and import
cc <- ChromatinContacts("data.cool") |> import()

# Focus on specific region
cc <- ChromatinContacts("data.cool", focus = "chr1:1-2e6") |> import()

# Multi-resolution cooler
cc <- ChromatinContacts("data.mcool", resolution = 10000) |> import()

# Add features
features(cc, "TADs") <- tads_granges
features(cc, "loops") <- loops_ginteractions
} # }