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Two additional datasets were sampled from this basic dataset, by removing apparent recombinant regions or haplotypes ('IM Reduced Dataset 1', and 'IM Reduced Dataset 2' – see methods and Table 1).
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Color bars indicate the center of all windows of size T for which the null hypothesis of the number of events per day in both datasets being sampled from the same distribution can be rejected at a 5% significance level.
Bold font marks cases where the value of the Anderson-Darling statistic A 2 is smaller than the critical level A 0.05 2 = 2.492 (large-sample approximation) and the hypothesis of two datasets being sampled from the same distribution can not be rejected at a 5% significance level.
The data used in simulation dataset were sampled from the abovementioned formulas (6) and (7), with all examples added with Gaussian noise at μ = 0, σ = 0.02(σ = 0.06, σ = 0.1).
The dog dataset was sampled from a dataset used for mapping quantitative trait loci underlying canine hip dysplasia [ 27, 28] and a dataset used to estimate heritability of canine hip dysplasia [ 30].
Following this strategy, our total dataset of 111 orthologous clades were sampled from those 10 non-housekeeping gene families.
Random subsets of various sizes up to 10 unique sequences were sampled from both datasets and processed by Hammock.
The jury evaluated the predictions using a normalized square error by comparing the predictions with a null-model in which the missing values were sampled from the dataset to estimate a p-value.
To obtain a more accurate estimate of parameter errors for small samples, the likelihood was maximised for 1000 bootstrapped samples, in which individuals were sampled from the dataset with replacement; see e.g. [ 33].
Z-slices were sampled from the dataset at 50 μm spacing and mean pore size over 20 slices was calculated using FIJI: after removal of outliers larger than 2 pixels, a watershed algorithm was applied to the dataset, to allow ellipse fit to each pore.
Added to the replication dataset were samples from eMERGE II by the Geisinger Health System, genotyped on Illumina Human Omni Express (875 pre-QC samples: 221 controls, 654 cases).
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