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

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

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

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