bioconductor-hicexperiment

name

bioconductor-hicexperiment

description

R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.

HiCExperiment

Workflows

Standard Workflow

library(HiCExperiment)
library(HiContactsData)

# Retrieve a sample cool file path
cool_file <- HiContactsData('yeast_wt', format = 'cool')

# Import the contact matrix as a HiCExperiment object
hic <- import(cool_file, format = 'cool', focus = 'I:20001-80000')

# Inspect the imported object
resolution(hic)

Input: A path to a .cool, .mcool, , or HiC-Pro contact matrix file. Output: A parsed object containing contact frequencies, genomic bins, and metadata.