parse_juicer_matrix {idr2d} | R Documentation

## 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.

[Package idr2d version 1.1.4 Index]