Selects top-weighted intra- and inter-chromosomal hyperedges per chromosome for visualization.
Usage
select(x, ...)
# S4 method for class 'MultiWayContacts'
select(
x,
n_intra = 5,
n_inter = 5,
n_multiways_filter = NULL,
chroms = NULL,
append = TRUE,
...
)Arguments
- x
MultiWayContacts with tidied hypergraph.
- ...
Additional arguments (not used).
- n_intra
Integer. Top intra-chromosomal hyperedges per chromosome (default: 5).
- n_inter
Integer. Top inter-chromosomal hyperedges per chromosome (default: 5). Quota increases if fewer intra hyperedges available.
- n_multiways_filter
Integer vector or NULL. Filter by specific contact orders, e.g.,
c(3,4)for 3-way and 4-way only (default: NULL).- chroms
Character or NULL. Filter by chromosome(s) (default: NULL).
- append
Logical. Append to existing selection (TRUE) or replace (FALSE, default: TRUE).
Value
MultiWayContacts with select_hypergraph slot containing selected
hyperedges plus type (intra/inter) and source_chrom columns.
Details
Per chromosome: select top n_intra intra-chromosomal and n_inter
inter-chromosomal hyperedges by weight. If insufficient intra hyperedges,
quota transferred to inter. Hyperedges deduplicated across chromosomes.
Examples
if (FALSE) { # \dontrun{
# Default: top 5 intra + 5 inter per chromosome
mc <- MultiWayContacts("sample.pairs.gz") |>
import() |> build() |> tidy() |> select()
# More hyperedges
mc <- mc |> select(n_intra = 10, n_inter = 10, append = FALSE)
# Filter by contact order
mc <- mc |> select(n_multiways_filter = c(3, 4), append = FALSE)
# Specific chromosomes
mc <- mc |> select(chroms = c("chr1", "chr2"), append = FALSE)
} # }