Read a .cool file into R and output the data in BEDPE format
The path to a .cool file on your disk.
.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.
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.
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## Not run: dat <- cooler2bedpe(path = "path/to/cool/file.cool") ## End(Not run)
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