Performance of random forest when SNPs are in linkage disequilibrium

  title={Performance of random forest when SNPs are in linkage disequilibrium},
  author={Yan A. Meng and Yi Yu and L. Adrienne Cupples and Lindsay A. Farrer and Kathryn L. Lunetta},
  journal={BMC Bioinformatics},
  pages={78 - 78}
Single nucleotide polymorphisms (SNPs) may be correlated due to linkage disequilibrium (LD). Association studies look for both direct and indirect associations with disease loci. In a Random Forest (RF) analysis, correlation between a true risk SNP and SNPs in LD may lead to diminished variable importance for the true risk SNP. One approach to address this problem is to select SNPs in linkage equilibrium (LE) for analysis. Here, we explore alternative methods for dealing with SNPs in LD: change… CONTINUE READING


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