glxnet
(Package: qtlnet) :
Generate and graph Glx network
This is the Glx network reported in Chaibub Neto et al 2008 and in Ferrara et al 2008. Age was used as an additive covariate and we allowed for sex by genotype interaction. The network differs slightly from the published network due to improved code.
We generate synthetic data (sample size 300) according to a DAG composed by 100 nodes and 107 edges (exactly as in Figure 1). Each phenotype node is affected by three QTLs, and we allow only additive genetic effects. The QTLs for each phenotype are randomly selected among 200 markers, with 10 markers unevenly distributed on each of 20 autosomes. We allowed different phenotypes to potentially share common QTLs. For each phenotype, the regression coefficients with other phenotypes are chosen uniformly between 0.5 and 1; QTL effects are chosen between 0.2 to 0.6; and residual standard deviations are chosen from 0.1 to 0.5. For each realization we apply the QDG algorithm to infer causal directions for the edges of the skeleton obtained by the PC-skeleton algorithm.
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