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Analyses within these four regions using a subset of SNPs in linkage equilibrium identified by MASEL algorithm, gave very similar results indicating that the linkage disequilibrium (LD) between SNPs is taken into proper account by the method implemented in MERLIN.
Estimates of recent migration rates (mBA) were inferred by the method implemented in the program BAYESASS V1.3 (Wilson and Rannala 2003).
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We took this point into account by using the method implemented in MERLIN [79].
Clustering analysis was performed using the package pheatmap in R (version 2.15.2) using read counts normalized by library size using the method implemented in edgeR.
To illustrate the distance-dependent decay of LD, we adopted the method implemented by Sharpiro et al., 2009 [ 14].
Samples were then centrifuged at 13,000 rpm for 7 min at 4 °C, following the method implemented by Takemori and Yamamoto [ 73].
To gain some intuition on how subgraphs can be generated, we first describe a simple combinatorial approach before we introduce the method implemented by GraTeLPy.
It is because that for the experiments suffering with these limitations it is not clear whether the genes at the significance statistical analysis are accurately measured by the methods implemented in the software that largely depends on reliable estimation of gene-specific biological variation or at least of the estimation of global biological variation across all genes [ 20].
At the opposite, the methods implemented by Bo and co-workers [ 29] remain the most efficient in all cases.
The next section briefly describes the methods implemented by the PALANTE Consortium to collect high-quality evidence and the case study.
The methods implemented by the analysis system have been previously used in several studies to investigate the quantitative properties of FAs in cells under various conditions.
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