GMAP: Identifying topologically accosciating domains and subdomains from Hi-C data

Overview

GMAP is an efficient algorithm to call topologically associating domains (TAD) and subdomains (subTAD) from normalized Hi-C contact map.

The method consists of three major steps. In step one, we fit a Gaussian mixture model with two components representing chromatin interactions within and outside of a domain. In step two, for each genomic bin, we determine if it is located at the boundary of blocks of dense chromatin interactions by performing a proportion test of observed contact counts within and between windows flanking the bin. In step three, we call chromatin domains based on the location and orientation of the candidate boundaries identified in step two.

Availability

The implementation rGAMP package, its instruction and updates are availabe through Github: R package rGMAP on Github

Reference

The detailed information of GMAP algorithm is described in the following paper:

Yu, W., He, B., & Tan, K. (2017). Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test. Nature Communications, 8, 535.