Electronic Journal of Statistics

Efficient block boundaries estimation in block-wise constant matrices: An application to HiC data

Vincent Brault, Julien Chiquet, and Céline Lévy-Leduc

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Abstract

In this paper, we propose a novel modeling and a new methodology for estimating the location of block boundaries in a random matrix consisting of a block-wise constant matrix corrupted with white noise. Our method consists in rewriting this problem as a variable selection issue. A penalized least-squares criterion with an $\ell_{1}$-type penalty is used for dealing with this problem. Firstly, some theoretical results ensuring the consistency of our block boundaries estimators are provided. Secondly, we explain how to implement our approach in a very efficient way. This implementation is available in the R package blockseg which can be found in the Comprehensive R Archive Network. Thirdly, we provide some numerical experiments to illustrate the statistical and numerical performance of our package, as well as a thorough comparison with existing methods. Fourthly, an empirical procedure is proposed for estimating the number of blocks. Finally, our approach is applied to HiC data which are used in molecular biology for better understanding the influence of the chromosomal conformation on the cells functioning.

Article information

Source
Electron. J. Statist., Volume 11, Number 1 (2017), 1570-1599.

Dates
Received: September 2016
First available in Project Euclid: 22 April 2017

Permanent link to this document
https://projecteuclid.org/euclid.ejs/1492826487

Digital Object Identifier
doi:10.1214/17-EJS1270

Mathematical Reviews number (MathSciNet)
MR3638971

Zentralblatt MATH identifier
1362.62012

Subjects
Primary: 62-07: Data analysis 62F30: Inference under constraints 62P10: Applications to biology and medical sciences
Secondary: 62F12: Asymptotic properties of estimators 62J07: Ridge regression; shrinkage estimators

Keywords
Change-points high-dimensional sparse linear model HiC experiments

Rights
Creative Commons Attribution 4.0 International License.

Citation

Brault, Vincent; Chiquet, Julien; Lévy-Leduc, Céline. Efficient block boundaries estimation in block-wise constant matrices: An application to HiC data. Electron. J. Statist. 11 (2017), no. 1, 1570--1599. doi:10.1214/17-EJS1270. https://projecteuclid.org/euclid.ejs/1492826487


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