To allow for comparison between LDSC, MAGMA, and DEPICT, we compared the P values that refer to the strength of association of a given cell type with a given phenotype. KI level 1, KI level 2, and 10x Genomics cell types were identified as significant after passing a Bonferroni corrected significance level of P < 0.05/(24*42), P < 0.05/(149*42), and P < 0.05/(16*42), respectively. We then counted the number of methods pointing to significant enrichment of specific cell types and report that number for both KI levels and 10x Genomics as our main outcome measure. Phenotypes implicating similar cell types were then identified by hierarchical clustering. We discuss these methods more elaborately below and in the Supplementary Methods.
