CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis
Figure 3
R/cape-derived interaction between Chromosome 1 and Chromosome 12.
(A) R/cape effect plots showing normalized phenotype values for each combination of the Chromosome 1 (D1Mit123) and Chromosome 12 (D12Mit150) genotypes. NON denotes a homozygous locus and Het denotes an NON/NZO heterozygote. Positive slopes correspond to Chromosome 1 effects, while differences between solid and dashed lines represent the Chromosome 12 effects. Positive and significant weight effects were detected for both loci, whereas effects on insulin were only significant for the Chromosome 1 marker. Neither locus had a significant effect on serum glucose. Significant epistasis was detected for weight, and appears as the convergence of solid and dashed lines for heterozygosity at the Chromosome 1 locus. Note that plotted data are not conditioned on maternal obesity, which was a covariate in the analysis. (B) Interaction network for variants on Chromosomes 1 and 12, extracted from Figure 2C, showing the significant suppressive interaction (red arrow) from the Chromosome 1 variant to the Chromosome 12 variant (gray circular nodes). Significant main effects (green arrows) link the source variants with the target phenotypes weight and insulin (square nodes labeled “I” and “W” respectively).