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Bioinformatics Advance Access originally published online on March 16, 2009
Bioinformatics 2009 25(10):1287-1292; doi:10.1093/bioinformatics/btp146
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation

Alun Thomas

Department of Biomedical Informatics, Division of Genetic Epidemiology, University of Utah, 391 Chipeta Way Suite D, Salt Lake City, UT 84108, USA


  Abstract

Motivation: Efficient models for genetic linkage disequilibrium (LD) are needed to enable appropriate statistical analysis of the dense, genome-wide single nucleotide polymorphism assays currently available.

Results: Estimation of graphical models for LD within a restricted class of decomposable models is shown to be possible using computer time and storage that scale linearly with the number of loci. Programs for estimation and for simulating from these models on a whole-genome basis are described and provided.

Availability: Java classes and source code for IntervalLD and GeneDrops are freely available over the internet at http://bioinformatics.med.utah.edu/~alun.

Contact: alun{at}genepi.med.utah.edu

Associate Editor: Alex Bateman

Received on November 13, 2008; revised on February 5, 2009; accepted on March 11, 2009

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