dot-importHicLib: Function to read in processed Hi-C interaction data generated...

In LTLA/fugi: Further Utilities for Genomic Interactions

Description

This function reads in the interaction data processed by [hiclib](https://bitbucket.org/mirnylab/hiclib). The data is extracted from hiclib and exported from its internal HDF5 format to text using h5dictToTxt.py. This function reads in the relevant files present in the directory and generates a data.table containing all of the information. It assumes that there are files with the following names in the directory: fragids1, chrms1, mids1, fraglens1, fragids2, chrms2, mids2, fraglens2, distances.

Usage

.importHicLib(dir, chr_names)

Arguments

dir	directory containing the output files generated by hiclib, extracted using h5dictToTxt.py
chr_names	ordered chromosome names (for renaming)

Value

data.table containing information on the individual interactions

LTLA/fugi documentation built on June 22, 2019, 8:50 p.m.