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. 2009 Mar 5;10:78. doi: 10.1186/1471-2105-10-78

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Copyright © 2009 Meng et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Proportion of replicates for which all rSNPs or best rSNP in haplotype, and HAPs are among the top-ranking X SNP/HAPs. (A) Top panels. Individual SNPs are used in the RF as the predictors. Left: The proportion of replicates for which both SNPs making up the haplotype are among the top X predictors. Right: The proportion of replicates where at least one of the two SNPs in the risk haplotype are among the top X predictors. (B) Middle panels: Left: true haplotypes are used in the RF as the predictors. The proportion of replicates where the true haplotype is among the top X predictors. Right: the haplotype phases are not known, and are resolved statistically. The predicted haplotypes are used in the RF as the predictors. (C) Bottom panels (left, right) show the four analyses for haplotypes consisting of two SNPs with r²= 0 and r²= 0.9.