RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method
Fig 4
An example of GWAS results for the repulsion scenario.
Manhattan plots of 4 GWAS methods (RAINBOW, Single-SNP GWAS, HGF (the number of groups is 2, the grouping method is UPGMA), and SKAT) for one simulation result of the Repulsion model. The black horizontal dashed lines represent the thresholds determined by the Benjamini-Hochberg method (FDR = 0.01) for each result of the Repulsion model. The red vertical dashed lines show the positions of QTN1, QTN2, and the purple ones show the position of QTN3. The red points show −log10(p) of causal SNPs or haplotypes including QTN1 and QTN2, and the purple ones show −log10(p) of QTN3 or haplotypes including QTN3.