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Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics

Fig 2

Comparing efficiency between VEGAS and Pascal.

a) Run times of VEGAS and Pascal (both options). Gene scores were computed on two GWAS (one HapMap imputed[23], one 1KG imputed[22,25]) for 18,132 genes on a single core. Pascal was compared to VEGAS for the HapMap imputed study and VEGAS2 for the 1KG-imputed study. For this plot, VEGAS and VEGAS2 were used with the default maximum number of Monte Carlo samples of 106 for both studies and additionally with 108 Monte Carlo samples for the HapMap imputed study. b) Scatter plot of -log10-transformed gene p-values for the sum gene scores obtained by VEGAS and Pascal, respectively. P-values above 10−6 are in excellent concordance. Below this value VEGAS could not give precise estimates, since it was run with the maximal number of Monte Carlo samples set to 108.

Fig 2