Chunk #17 — MATERIALS AND METHODS — Admixture mapping:

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Genome-wide admixture mapping of DSM-IV alcohol dependence, criterion count, and the self-rating of the effects of ethanol in African American populations.

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The following procedure was used to determine the GWS threshold. First, matSpD was used to account for correlations across the four phenotypes by spectral decomposition of the correlation matrix (Li & Ji, 2005; Nyholt, 2004), resulting in 2.52 effective independent tests. Second, using the autocorrelation function of the R package CODA (Plummer, Best, Cowles, & Vines, 2005), 273.82 effective African ancestry blocks were estimated across the entire genome using a combined sample from all cohorts. Therefore, the GWS threshold was determined as 0.05/(2.52*273.82)=7.25E-05.