MultiWayContacts S4 class

S4 class for multi-way chromatin contacts from long-read sequencing (Pore-C, Micro-C XL). Represents interactions as hypergraphs where reads connect multiple genomic loci.

Constructor for MultiWayContacts from .pairs files.

Usage

MultiWayContacts(pairs_path = NULL, focus = NULL)

Arguments

pairs_path

Character. Path to .pairs or .pairs.gz file.

focus

Character or NULL. Chromosome(s) to analyze (NULL for genome-wide).

Details

Workflow: Create → Import → Build → Tidy → Select → Visualize

Key features:

• Hypergraph representation: reads as hyperedges connecting bins

• Sparse matrix storage for memory efficiency

• Multiple weight normalizations

• Flexible filtering by order, chromosome, and weight

Slots

pairs_path

Character. Path to .pairs file.

pairs

Data.frame or NULL. Loaded pairs data.

bin_size

Integer or NULL. Genomic bin size in base pairs.

focus

Character or NULL. Chromosome(s) to analyze.

hypergraph

dgCMatrix or NULL. Sparse incidence matrix (bins × hyperedges).

weights

Data.frame. Hyperedge weights with normalizations (raw, log, by_order, minmax).

bin_info

Data.frame. Genomic bin information.

hyperedge_reads

SimpleList. Read names per hyperedge.

multiways

Numeric. Contact count per hyperedge.

tidied_hypergraph

Data.frame or NULL. Long-format hypergraph.

select_hypergraph

Data.frame or NULL. Selected hyperedges for plotting.

See also

MultiWayContacts(), import-MultiWayContacts, build(), tidy(), select(), gghypergraph()

Examples

if (FALSE) { # \dontrun{
# Basic usage
mc <- MultiWayContacts("sample.pairs.gz")

# Focus on chromosome
mc <- MultiWayContacts("sample.pairs.gz", focus = "chr1")

# Complete workflow
mc <- MultiWayContacts("sample.pairs.gz", focus = "chr1") |>
  import() |>
  build(bin_size = 1000000L) |>
  tidy() |>
  select(n_intra = 10, n_inter = 5) |>
  gghypergraph()
} # }