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Bioinformatics Advance Access published online on June 14, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti536
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received May 26, 2005
Accepted June 8, 2005

Applications note

HEGESMA: genome search meta-analysis and heterogeneity testing

Elias Zintzaras 1* and John P. A. Ioannidis 2

1 Department of Biomathematics, University of Thessaly School of Medicine, Larissa, Greece
2 Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece; Department of Medicine, Tufts University School of Medicine, Boston, Mass., USA

* To whom correspondence should be addressed.
Elias Zintzaras, E-mail: zintza{at}med.uth.gr


  Abstract

Summary: HEGESMA is a comprehensive software for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across multiple genome scans, and for testing the heterogeneity of the results of each bin across scans. The program provides as an output the average of ranks and three heterogeneity statistics, as well as corresponding significance levels. Statistical inferences are based on Monte Carlo permutation tests. The program allows both unweighted and weighted analysis with the weights for each study specified by the user. Furthermore, the program performs heterogeneity analyses restricted to the bins with similar average ranks.

Availability: http://biomath.med.uth.gr.


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