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Figure 2 | BMC Proceedings

Figure 2

From: Principal-component-based population structure adjustment in the North American Rheumatoid Arthritis Consortium data: impact of single-nucleotide polymorphism set and analysis method

Figure 2

Q-Q plot of -log 10 ( p -value) for analyses. Quantile-Quantile plot of -log10(p-value) for Methods A-F as described in Methods. For each analysis, we plot the negative -log10(p-value) for all genome-wide SNPs, excluding the SNPs in the MHC. Black, Method (A) - logistic regression adjusting for the DRB locus (inflation factor λ = 1.24); Red, Method (B) - logistic regression adjusting for the DRB locus and PC1-4 as continuous covariates (λ = 1.03); Green, Method (C) - logistic regression adjusting for the DRB locus and PC cluster (λ = 1.04); Blue, Method (D) - logistic regression adjusting for the DRB locus, PC1-4 as continuous covariates, and PC cluster (λ = 1.03); Purple, Method (E) - PSAT with disease probability assigned based on clustering on PC1-4 (λ = 1.15); and Orange, Method (F) - genomic control using the logistic model adjusting for the DRB locus (λ = 1.00).

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BMC Proceedings

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