Jump to ContentJump to Main Navigation
Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics$
Users without a subscription are not able to see the full content.

Christine Sinoquet and Raphaël Mourad

Print publication date: 2014

Print ISBN-13: 9780198709022

Published to Oxford Scholarship Online: December 2014

DOI: 10.1093/acprof:oso/9780198709022.001.0001

Show Summary Details
Page of

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2020. All Rights Reserved. An individual user may print out a PDF of a single chapter of a monograph in OSO for personal use. date: 19 January 2020

Modeling Linkage Disequilibrium with Decomposable Graphical Models

Modeling Linkage Disequilibrium with Decomposable Graphical Models

Chapter:
(p.247) Chapter 10 Modeling Linkage Disequilibrium with Decomposable Graphical Models
Source:
Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics
Author(s):

Haley J. Abel

Alun Thomas

Publisher:
Oxford University Press
DOI:10.1093/acprof:oso/9780198709022.003.0010

This chapter describes the use of decomposable graphical models (DGMs) to represent the dependences within genetic data, or linkage disequilibrium (LD), prior to various downstream applications. First, general learning algorithms are reviewed: schemes based on Markov chains Monte Carlo and related simulated annealing strategies are described. However, for tractable processing of high-dimensional data, it is shown that sampling the space of DGMs is efficiently replaced with the sampling of representations of DGMs — the junction trees. Then, a first application is considered: the phase imputation for diploid data, which consists in inferring the latent genetical phased haplotypes underlying the observed genetical unphased genotypes. In particular, it is shown that in the case of diploid data, decoupling the model estimation step from the phasing step allows scalability of the whole learning process. The chapter ends with the illustration of the potentialities of DGMs through four applications.

Keywords:   linkage disequilibrium, phase imputation, decomposable graphical models

Oxford Scholarship Online requires a subscription or purchase to access the full text of books within the service. Public users can however freely search the site and view the abstracts and keywords for each book and chapter.

Please, subscribe or login to access full text content.

If you think you should have access to this title, please contact your librarian.

To troubleshoot, please check our FAQs , and if you can't find the answer there, please contact us .