Alun Thomas1. 1. Department of Biomedical Informatics, Division of Genetic Epidemiology, University of Utah, 391 Chipeta Way Suite D, Salt Lake City, UT 84108, USA. alun@genepi.med.utah.edu
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.
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.
Authors: Stacey Knight; Ryan P Abo; Haley J Abel; Deborah W Neklason; Therese M Tuohy; Randall W Burt; Alun Thomas; Nicola J Camp Journal: Ann Hum Genet Date: 2012-09-19 Impact factor: 1.670