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Bioinformatics Advance Access originally published online on May 21, 2008
Bioinformatics 2008 24(14):1603-1610; doi:10.1093/bioinformatics/btn239
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis

Sophia S. F. Lee 1,2, Lei Sun 1,3, Rafal Kustra 1 and Shelley B. Bull 1,2,*

1Department of Public Health Sciences, University of Toronto, Toronto M5T 3M7, 2Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto M5G 1X5 and 3Genetics and Genomic Biology, The Hospital for Sick Children Research Institute, Toronto M5G 1L7, Canada

*To whom correspondence should be addressed.


  Abstract

Motivation: We developed an EM-random forest (EMRF) for Haseman–Elston quantitative trait linkage analysis that accounts for marker ambiguity and weighs each sib-pair according to the posterior identical by descent (IBD) distribution. The usual random forest (RF) variable importance (VI) index used to rank markers for variable selection is not optimal when applied to linkage data because of correlation between markers. We define new VI indices that borrow information from linked markers using the correlation structure inherent in IBD linkage data.

Results: Using simulations, we find that the new VI indices in EMRF performed better than the original RF VI index and performed similarly or better than EM-Haseman–Elston regression LOD score for various genetic models. Moreover, tree size and markers subset size evaluated at each node are important considerations in RFs.

Availability: The source code for EMRF written in C is available at www.infornomics.utoronto.ca/downloads/EMRF

Contact: bull{at}mshri.on.ca

Supplementary information: Supplementary data are available at www.infornomics.utoronto.ca/downloads/EMRF

Associate Editor: Martin Bishop

Received on November 15, 2007; revised on May 16, 2008; accepted on May 17, 2008

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