Figure 3
From: Performance of random forest when SNPs are in linkage disequilibrium
Proportion of replicates for which all rSNPs and/or LD.rSNPs are among the top-ranking X SNPs. The data were simulated using model H4M4 with K4S4 analysis design. (A) Top panels: the proportion of replicates for which each rSNP or one of its corresponding LD.rSNPs is among the top X SNPs ("rSNPs/LD.rSNPs"). Left panel: RF0:IM0; right panel: RF0:IM1. (B) Middle panels: using RF0:IM1, we compare the proportion of replicates for which each rSNP or at least one corresponding LD.rSNP was among the top-ranking X SNPs, the proportion considering only rSNPs ("rSNPs with LD.rSNPs"), and the proportion where there are no rSNPs in the dataset ("rSNPs, no LD.rSNPs"), with example of 1 SNP and 4 SNPs in LD with each rSNP. (C) Bottom panels: we compare the four combinations of original and revised RF and original and revised IM, with examples for 1 and 4 LD.rSNPs.