Plink scoring function mechanism
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2.6 years ago

To use --score ScoreFile function, in ScoreFile, we need SNP ID, effect allele and effect size. Say, if the effect allele is the minor allele, then the score contributed by the SNP should be effective size * dosage (effect allele); however, if the effect allele is not the minor allele, then how to calculate the contribution of the SNP. It should be effect size * (2 - dosage (effect allele)), or effect size * - dosage(effect allele)?

plink scoring • 653 views
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