Fig. 3

Results for blood cell methylomes. a–e WB1 data set. a Selection of parameters k and λ by cross-validation. b Matching the WB1 LMCs to PureBC methylomes (k=20, λ=0.001). Here and below the dendrogram visualizes agglomerative hierarchical clustering analysis with a correlation-based distance measure and average linkage. c Matching the LMCs from the WB2 data set (k=20, λ=0.001) to the PureBC methylomes. d Matching the WB1 and WB2 LMCs to each other. Pairs of reproducible LMCs also matching to the reference profiles are highlighted by red segments. Green segments mark reproducible LMCs that do not directly match any of the reference profiles. e Adjustment of the association analysis for rheumatoid arthritis in the full Liu et al. data set [35]. Each curve is a Q-Q plot of P values observed in the corresponding analysis versus the expected P values sampled from a uniform distribution. f–h PureBC data. f Selection of parameters k and λ by cross-validation. g Heat map of recovered proportions in PureBC data (k=15, λ=0.001). Rows represent LMCs while columns correspond to individual purified samples. The order of blood donors is the same within column sets, corresponding to one cell type. h Methylation differences in naive versus memory B cells at CpGs differentially methylated between LMC2 and LMC13 from the PureBC data set. WGBS methylation profiles of naive and memory B cells were obtained from BLUEPRINT. The value for memory B cells is an average of three WGBS samples. A Wilcoxon ranked sum test was used to test the null hypothesis that WBGS methylation calls are the same in naive and memory cells at their respective CpG positions