parse_hic_pro_matrix {idr2d} | R Documentation

## Parse .matrix and .bed files from HiC-Pro for IDR2D analysis

### Description

This function is used to convert the contact matrix from a HiC-Pro pipeline analysis run into an IDR2D compatible format. It takes one .matrix and one .bed file per replicate from HiC-Pro and returns the contact matrix for a specific chromosome for IDR2D analysis (see `estimate_idr2d_hic`)

### Usage

    parse_hic_pro_matrix(matrix_file, bed_file, chromosome = "chr1")

### Arguments

`matrix_file` | path to .matrix file from HiC-Pro analysis run
`bed_file` | path to .bed file from HiC-Pro analysis run
`chromosome` | chromsome name to be analyzed, defaults to UCSC chromosome 1 (`"chr1"`)

### 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

Servant, N., Varoquaux, N., Lajoie, B.R. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16, 259 (2015) doi:10.1186/s13059-015-0831-x

[Package idr2d version 1.2.2 Index]