Open a .cool or .mcool HDF5 contact matrix file

Supports both .cool (single-resolution) and .mcool (multi-resolution) files produced by cooler / HiCExplorer.

Usage

open_h5(path, resolution = NULL, max_fetch_bp = 5000000L)

Arguments

path

Character. Path to the .cool or .mcool file.

resolution

Integer or NULL. For .mcool files, which resolution to open. When NULL, the coarsest available resolution is used for the probe; you must set resolution explicitly in $fetch().

max_fetch_bp

Integer. Maximum genomic span per $fetch() call. Default 5e6 (5 Mb).

Value

A SeqH5 S3 object with $fetch() and $fetch_binned() methods.