Jump to ContentJump to Main Navigation
Show Summary Details
More options …

The International Journal of Biostatistics

Ed. by Chambaz, Antoine / Hubbard, Alan E. / van der Laan, Mark J.


IMPACT FACTOR 2017: 0.840
5-year IMPACT FACTOR: 1.000

CiteScore 2017: 0.97

SCImago Journal Rank (SJR) 2017: 1.150
Source Normalized Impact per Paper (SNIP) 2017: 1.022

Mathematical Citation Quotient (MCQ) 2016: 0.09

Online
ISSN
1557-4679
See all formats and pricing
More options …

Comparison of Estimators for Measures of Linkage Disequilibrium

Markus Scholz / Dirk Hasenclever
Published Online: 2010-01-06 | DOI: https://doi.org/10.2202/1557-4679.1162

The measurement of biallelic pair-wise association called linkage disequilibrium (LD) is an important issue in order to understand the genomic architecture. A plethora of measures of association in two by two tables have been proposed in the literature. Beside the problem of choosing an appropriate measure, the problem of their estimation has been neglected in the literature. It needs to be emphasized that the definition of a measure and the choice of an estimator function for it are conceptually unrelated tasks.In this paper, we compare the performance of various estimators for the three popular LD measures D', r and Y in a simulation study for small to moderate samples sizes (N<=500). The usual frequency-plug-in estimators can lead to unreliable or undefined estimates. Estimators based on the computationally expensive volume measures have been proposed recently as a remedy to this well-known problem. We confirm that volume estimators have better expected mean square error than the naive plug-in estimators. But they are outperformed by estimators plugging-in easy to calculate non-informative Bayesian probability estimates into the theoretical formulae for the measures. Fully Bayesian estimators with non-informative Dirichlet priors have comparable accuracy but are computationally more expensive.We recommend the use of non-informative Bayesian plug-in estimators based on Jeffreys' prior, in particular when dealing with SNP array data where the occurrence of small table entries and table margins is likely.

Keywords: measures of linkage disequilibrium; two by two contingency tables; estimation problem; Dirichlet prior

About the article

Published Online: 2010-01-06


Citation Information: The International Journal of Biostatistics, Volume 6, Issue 1, ISSN (Online) 1557-4679, DOI: https://doi.org/10.2202/1557-4679.1162.

Export Citation

©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston.Get Permission

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

[1]
Karianne Fjeld, Frank Ulrich Weiss, Denise Lasher, Jonas Rosendahl, Jian-Min Chen, Bente B Johansson, Holger Kirsten, Claudia Ruffert, Emmanuelle Masson, Solrun J Steine, Peter Bugert, Miriam Cnop, Robert Grützmann, Julia Mayerle, Joachim Mössner, Monika Ringdal, Hans-Ulrich Schulz, Matthias Sendler, Peter Simon, Paweł Sztromwasser, Janniche Torsvik, Markus Scholz, Erling Tjora, Claude Férec, Heiko Witt, Markus M Lerch, Pål R Njølstad, Stefan Johansson, and Anders Molven
Nature Genetics, 2015, Volume 47, Number 5, Page 518

Comments (0)

Please log in or register to comment.
Log in