Fig. 2: Manhattan and QQ plots of MWAS using linear or mixed linear regression models, for the Australian ALS samples (Ncases = 613 and Ncontrols = 782). | npj Genomic Medicine

Fig. 2: Manhattan and QQ plots of MWAS using linear or mixed linear regression models, for the Australian ALS samples (Ncases = 613 and Ncontrols = 782).

From: Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

Fig. 2

a From top to bottom row: Manhattan plots using linear regression, linear regression with 10 principal components calculated from the ORM as fixed effects, MOA, and MOMENT. Red circles represent probes with p < 1 × 10−5; red crosses represent probes with p < 3.1 × 10−7 genome-wide significant threshold. Solid dark blue line mark p < 3.1 × 10−7 and dashed sky-blue line marks p < 1 × 10−5. b QQ-plots showing the expected and observed −log(p) in each model. We calculated the genomic inflation factor (λ) as the median of χ2 test statistics of all probes divided by its expected value under the null. λLinear = 1.19, λLinear_with_PCs = 1.1, λMOA = 1.01, λMOMENT = 1.02.

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