For visualization purposes we aggregated the 127 cell types into five clusters, using k-means clustering. The number of clusters was chosen based on the number of different sample types annotated by Roadmap (primary cell, primary culture, primary tissue, cell line, ESC derived). A heatmap of the difference in fold enrichment between iPSC-specific and non-specific eQTLs (DIFF = FEspecific - FEnonspecific) was generated with the pheatmap package in R (Fig. 4d) in order to assess how well our definition of iPSC-specific enriches for functional elements active in stem cells.
