Fig. 2

Capturing population structure in the GALA II data using an unsupervised approach. a The first two PCs of the genotypes, considered as the gold standard, separate the samples into two subpopulations: Puerto Ricans (in blue) and Mexicans (in red), b the first two PCs of the methylation levels (methylation PCs) cannot reconstruct the separation found with the genotype data, c recalculating the first two PCs after applying a feature selection based on proximity of CpGs to nearby SNPs as was proposed by Barfield et al. [21], d the first two PCs of the methylation after adjusting the data for cell-type composition (adjusted methylation PCs) can reconstruct most of the separation found in the genotypes, e using adjusted methylation PCs after excluding the 70,889 polymorphic sites from the data, f using adjusted methylation PCs after excluding the 167,738 probes containing at least one common SNP