HiCseg


Two-dimensional segmentation for analyzing Hi-C data

Motivation: The spatial conformation of the chromosome has a deep influence on gene regulation and expression. Hi-C technology allows the evaluation of the spatial proximity between any pair of loci along the genome. It results in a data matrix where blocks corresponding to (self-)interacting regions appear. The delimitation of such blocks is critical to better understand the spatial organization of the chromatin. From a computational point of view, it results in a 2D segmentation problem.

 

Results: We focus on the detection of cis-interacting regions, which appear to be prominent in observed data. We define a block-wise segmentation model for the detection of such regions. We prove that the maximization of the likelihood with respect to the block boundaries can be rephrased in terms of a 1D segmentation problem, for which the standard dynamic programming applies. The performance of the proposed methods is assessed by a simulation study on both synthetic and resampled data. A comparative study on public data shows good concordance with biologically confirmed regions.

 

Availability and implementation: The HiCseg R package is available from the Comprehensive R Archive Network and from the Web page of the corresponding author.


Informations générales
Suivi
Maintenu
Informations spécifiques
Langage(s) de développement
R
Langage(s) d'interface
R
N° de version courante
V1.1
Date de la version courante
OS supporté
Type de licence


Porteur(s)
Unité
MIA-Paris
Auteur(s)
Contact
celine.levy-leduc@agroparistech.fr


 

 

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