卓越 java 李林_李林

TADBD: a sensitive and fast method for detection of TAD boundaries

Abstract

Topological Associated Domain (TAD) is a self-interacting genomic block. The detection of TAD boundaries on Hi-C contact matrix is one of the most important issues in the analysis of 3D genome architecture at TAD level. Here, we present TADBD, a sensitive and fast computational method for detection of TAD boundaries on Hi-C contact matrix. It implements a Haar-based algorithm considering Haar diagonal template, the acceleration via a compact integrogram, multi-scale aggregation at template size, and statistical filtering. Compared with the other six popular methods based on simulated and experimental Hi-C data, TADBD is competitive in terms of accuracy, speed and robustness. In addition, a new R package TADBD is freely given out online.

1> Datasets

Simulated data:

Yu, W., He, B. and Tan, K. (2017) Identifying topologically associating domains and ubdomains by Gaussian Mixture model And

Proportion test, Nat Commun, 8, 535.https://bitbucket.org/mforcato/hictoolscompare/src/master/

Real data:

Rao, S.S.P., et al. (2014) A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping, Cell, 159, 1665-1680.

2> TADBD

Description:

An R package for detection of TAD boundaries

Depends:

R (>= 3.5.1)

Example:

rm(list=ls())

library(TADBD)

species

chr

resolution

options(scipen = 999)

data(hicdata)

hicmat

df_result

#Output a text file

Output(df_result, species, chr, resolution)

#Output a heatmap

Output(df_result, species, chr, resolution, outxtfile="./result", bheatmap = T, heatmapfile="./heatmap", hicmat)