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Chunk #13 — Methods — Statistical analysis

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Polygenic risk for alcohol dependence associates with alcohol consumption, cognitive function and social deprivation in a population-based cohort.
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All variables were transformed towards normality where necessary using the Box‐Cox transformation procedure implemented in the MASS package in R (Venables & Ripley 2002). The ASReml‐R (www.vsni.co.uk/software/asreml) software package was used to implement mixed linear model association analyses. Family structure was fitted as a random effect by creating an inverse of a relationship matrix using pedigree kinship information. All variables were scaled to have a mean of 0 and a standard deviation of 1, and the reported values of beta are standardized. Wald's conditional F‐test was used to calculate P‐values for fixed effects. The proportion of variance explained by PGRS was calculated by taking the change in the sum of the residual variance and the additive genetic variance after removing the PGRS from the model, then dividing this by the sum of residual variance and the additive genetic variance. Pearson's correlations were used to determine the correlation between the two PGRS and alcohol consumption and cognitive/demographic variables in unrelated individuals (n = 6413) (Supporting Information Table S1).