MAGMA: Generalized Gene-Set Analysis of GWAS Data
Fig 2
Comparison of self-contained gene-set analysis results.
Gene set—log10 p-values from the CD data self-contained gene-set analysis for MAGMA and PLINK. Panel (A) shows the PLINK-avg (no pruning) results compared with the MAGMA-main analysis, panel (B) the PLINK-prune results compared with the MAGMA-main analysis and (C) the two PLINK analyses compared to each other. P-values below 10–8 are truncated to 10–8 (grey points) to preserve the visibility of the other points.