cooler2bedpe: Read a .cool file into R and output the data in BEDPE format

In dozmorovlab/HiCcompare: HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

Read a .cool file into R and output the data in BEDPE format

Description

Read a .cool file into R and output the data in BEDPE format

Usage

cooler2bedpe(path)

Arguments

path	The path to a .cool file on your disk.

Details

.cool files are HDF5 containers that store Hi-C data. Many public Hi-C datasets are available in .cool format on the mirnylab ftp site ftp://cooler.csail.mit.edu/coolers. To use these files in HiCcompare simply download the .cool file and read it into R using this function. This function will dump the contents of the file and format them into BEDPE format in R. The resulting object cant then be used in HiCcompare.

Value

A list with two items. Item 1, "cis" contains the intra-chromosomal contact matrices, one per chromosome. Item 2, "trans" contains the inter-chromsomal contact matrix.

Examples

## Not run: 
 dat <- cooler2bedpe(path = "path/to/cool/file.cool")

## End(Not run)

dozmorovlab/HiCcompare documentation built on June 30, 2023, 3:09 a.m.