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The pair-potential was calculated using a distance bin of 0.25 Å.
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Distance intervals were created using a bin distance of 1.0%.
The variation in r2 in a distance bin is partly because of the variation in LD in different genomic regions.
To study the effect of bin size, we compare the power curves of the generalized UniFrac distances using a smaller bin size of 0.01 (∼700 OTUs per sample) or a larger bin size of 0.03 (∼80 OTUs per sample).
A minimum spanning tree (MST) was constructed using the default distance bin size of 100%.
Distribution histograms were plotted using a 0.01 bin size.
Using a MAF binning threshold of 0.03, we binned genes, pathways, and intergenic regions.
Their values were derived for each distance bin using a search code based on the downhill simplex Nelder Mead method, combined with a singular value decomposition (SVD) algorithm (Press et al. 1992) to calculate the linear coefficients at each simplex step.
which uses a bin width of 5 out to a radial distance of 100, and then re-bins these values to ensure at least 20 counts per bin.
Bins were defined using a 10-year risk of CAD: Bin 1, < 5%; Bin 2, 5-10%; Bin 3, >10%; Bin 4, known CAD.
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