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

cooler2bedpe(path)

Arguments

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

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.

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.

Examples

if (FALSE) {
 dat <- cooler2bedpe(path = "path/to/cool/file.cool")
}