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Using single locus score tests, 15 common SNPs were found to be significantly associated with "body fatness" measures such as weight, BMI, hip and waist circumferences with P-values ranging from 0.0004 to 0.01.
In contrast to the mutation score, the locus score does not depend on the particular mutation but only on its location.
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These coefficients are then used as locus scores.
Data quality analyses indicated only minor issues concerning locus scoring accuracy, nonrandom association of loci, and population admixture.
One locus scoring "strong" (≥ 1 – 1.5) was found in each of Thun, Brienz and Zuerich flocks and two in Maggiore.
Additionally, the multi-locus linear methods do not implicitly allow for the inclusion of epistatic interactions in the locus scoring process, while RF does.
Analogously, we also define locus scores S w and weighted scores exp(S w)Δ s (the rationale behind the nonlinear weighting function is discussed later).
The other 18 samples comprised (i) 15 with ≥1 locus scoring <10 but identified as a known S. sonnei allele and (ii) 3 with novel locus variants (each having one locus for which the highest scoring match (scores 20 160) differed from a known S. sonnei allele by one mismatching base).
We tested the genetic association of the remaining 29 SNPs with each of the adjusted anthropometric trait using the single-locus score test under additive model (1df test).
As a positive example, one may generalize (5) into a two-locus score function.
We define and discuss several families of one-locus score function definitions, i.e. the implicit, explicit and optimal ones.
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