Import multi-way contact data

Imports multi-way chromatin contact data from a .pairs file into a MultiWayContacts object. The method loads pairwise contacts from long-read sequencing experiments (e.g., Pore-C).

Usage

# S4 method for class 'MultiWayContacts,ANY,ANY'
import(con, format, text, inter_chrom = FALSE, ...)

Arguments

con

A MultiWayContacts object containing the path to the pairs file and optional focus regions.

format

Logical indicating whether to include inter-chromosomal contacts. This parameter is used as the second positional argument for convenience. Default is FALSE.

text

Not used. Included for compatibility with the generic.

inter_chrom

Logical. If TRUE, includes inter-chromosomal contacts. If FALSE (default), only intra-chromosomal contacts are loaded. If format is provided, it overrides this parameter.

...

Additional arguments (currently not used).

Value

A MultiWayContacts object with the pairs slot populated by a data frame containing:

• read_name: Unique identifier for each read

• chrom1, chrom2: Chromosomes for each contact

• pos1, pos2: Genomic positions for each contact

Details

The function loads pairwise contact data from a .pairs file format (typically .pairs.gz). If a focus chromosome is specified in the MultiWayContacts object, only contacts involving that chromosome are loaded.

When inter_chrom = FALSE, reads that contain any inter-chromosomal contacts are completely removed from the dataset to ensure clean intra-chromosomal analysis.

The pairs file is read using optimized C code for efficient parsing of large files.

For convenience, the inter_chrom parameter can be provided as the second positional argument: import(mc, TRUE) is equivalent to import(mc, inter_chrom = TRUE).

Examples

if (FALSE) { # \dontrun{
# Basic import (intra-chromosomal only)
mc <- MultiWayContacts("sample.pairs.gz")
mc <- import(mc)

# Using pipe operator
mc <- MultiWayContacts("sample.pairs.gz") |> import()

# Include inter-chromosomal contacts
mc <- import(mc, inter_chrom = TRUE)

# Convenient syntax
mc <- import(mc, TRUE)

# Import with focus on specific chromosome
mc <- MultiWayContacts(
  "sample.pairs.gz",
  focus = "chr1"
) |> import()

# Check imported data
head(mc@pairs)
} # }