Imports interaction data from cooler file into ChromatinContacts object.
Usage
# S4 method for class 'ChromatinContacts,ANY,ANY'
import(con, format, text, balance_column = "weight", ...)Arguments
- con
ChromatinContacts object with cooler file path.
- format
Character. Balance column name for normalization (default:
"weight"). Can be provided as second argument for convenience.- text
Not used (compatibility).
- balance_column
Character. Balance column name (overridden by
formatif provided).- ...
Additional arguments (not used).
Value
ChromatinContacts with interactions slot populated by GInteractions
containing bin_id1, bin_id2, count, and balanced columns.
Details
Loads Hi-C data from cooler file. If focus regions are specified, only those interactions are loaded. Balance weights (e.g., "weight", "KR", "VC") are used to normalize raw counts. Warning issued if balance column not found.
Shorthand: import(cc, "KR") is equivalent to
import(cc, balance_column = "KR").
Examples
if (FALSE) { # \dontrun{
# Basic import
cc <- ChromatinContacts("sample.cool") |> import()
# With specific balance column
cc <- import(cc, "KR")
# Focus region (more efficient)
cc <- ChromatinContacts("sample.cool", focus = "chr1:1-5e6") |> import()
} # }