In order to test whether the cell type ranking obtained using MAGMA and LDSC in the Zeisel et al. dataset 30 were similar, we computed the Spearman rank correlation of the cell types association strength (−log10P) between the two methods for each complex trait. The Spearman rank correlation was strongly correlated with λGC (a measure of the deviation of the GWAS test statistics from the expected) (Spearman ρ=0.89) (Figure S29) and with the average number of cell types below our stringent significance threshold (Spearman ρ=0.92), indicating that the overall ranking of the cell types is very similar between the two methods, provided that the GWAS is well powered (Figure S30). In addition, we found that λGC was strongly correlated with the strength of association of the top tissue (−log10P) (Spearman ρ=0.88) (Figure S31), as well as with the effect size (beta) of the top tissue (Spearman ρ=0.9), indicating that cell type – trait associations are stronger for well powered GWAS. The significance level (−log10P) was also strongly correlated with the effect size (Spearman ρ=0.996) (Figure S31) for the top cell type of each trait.
