cool2IntSet: Read .cool/.mcool sparse matrix into a InteractionSet object

In dovetail-genomics/coolR: Convert Cooler HDF5 Contact Matrix To InteractionSet Objects

Description

This function reads HiC contact matrix file(s) created by the cooler application (https://github.com/mirnylab/cooler) stored in a HDF5 data storage and converts them to an InteractionSet object for all detected pair of genomic bins with the counts of reads in these bin pairs

Usage

cool2IntSet(files, res = NULL, cores = detectCores())

Arguments

files	A character vector of paths to HDF5 stored cool (uni-dimension) or mcool (multi-dimension sparse matrix). If using a multi-dimesion, the resolution of one of the dimension need to be passed to res.
res	'NULL' if using a uni-dimensional cool file or the resolution of one of layer in the mcool file
cores	An integer for the number of parallel thread to convert the file

Value

An InteractionSet of all common pairs with the number of interaction for each pairs

dovetail-genomics/coolR documentation built on Oct. 7, 2020, 1:33 a.m.