parse_juicer_matrix: Parse .hic files from Juicer for IDR2D analysis

In kkrismer/idr2d: Irreproducible Discovery Rate for Genomic Interactions Data

Parse .hic files from Juicer for IDR2D analysis

Description

parse_juicer_matrix uses the Python package hic-straw internally to read .hic contact matrix files (see hic-straw on PyPI or the Aiden lab GitHub repository for more information).

The contact matrix is subdivided into blocks, where the block size is determined by resolution. The reads per block are used to rank blocks and replicate blocks are easily matched by genomic location.

Usage

parse_juicer_matrix(
  hic_file,
  resolution = 1e+06,
  normalization = c("NONE", "VC", "VC_SQRT", "KR"),
  chromosome = "chr1",
  use_python = NULL,
  use_virtualenv = NULL,
  use_condaenv = NULL
)

Arguments

hic_file	path to .hic file (either local file path or URL).
resolution	block resolution of Hi-C contact matrix in base pairs, defaults to 1,000,000 bp (usually one of the following: 2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000)
normalization	normalization step performed by Python package hic-straw, one of the following: "NONE", "VC", "VC_SQRT", "KR".
chromosome	chromsome name to be analyzed, defaults to UCSC chromosome 1 ("chr1")
use_python	if Python is not on PATH, specify path to Python binary here (see use_python)
use_virtualenv	if Python package hic-straw is not in base virtualenv environment, specify environment here (see use_virtualenv)
use_condaenv	if Python package hic-straw is not in base conda environment, specify environment here (see use_condaenv)

Value

Data frame with the following columns:

column 1:	chr	character; chromosome of block (e.g., "chr3")
column 2:	region1	integer; genomic location of side A of block in Hi-C contact matrix
column 3:	region2	integer; genomic location of side B of block in Hi-C contact matrix
column 4:	value	numeric; (normalized) read count in block

References

Neva C. Durand, James T. Robinson, Muhammad S. Shamim, Ido Machol, Jill P. Mesirov, Eric S. Lander, and Erez Lieberman Aiden. "Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom." Cell Systems 3(1), 2016.

kkrismer/idr2d documentation built on Feb. 7, 2024, 2:23 p.m.