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Chunk #24 — Materials and Methods — Statistical analysis — Selection of PC for PS correction

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Population substructure and control selection in genome-wide association studies.
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The permutation procedure used in step 2.a is designed to determine if adjusting for the PC u (l) in addition to those already included in E results into a significantly lower over-dispersion factor, compared with the level expected under the situation when the additional covariate to be adjusted for is randomly generated, and thus has no contribution to the correction of PS. The rationale is that we should adjust for u (l) whenever its inclusion makes a “significant” impact on the correction of PS. Here are the basic steps for the permutation procedure used in the lth iteration of the search algorithm.