Figure 3.—
Randomly sampled sparse directed acyclic graph (DAG) composed of 100 nodes (phenotypes) connected by 107 edges, using the randomDAG function from the pcalg R package (R Development Core Team 2006). We generated data according to this network, adopting two or three QTL (not shown) per phenotype. This network demonstrates many features that can be inferred with varying degrees of difficulty by the PC algorithm. For instance, nodes organized in an unshielded collider pattern (Shipley 2002) such as 
are easier to direct than nodes organized in a bifurcation or line pattern such as 
and 
. Figure 8 compares the performances of the QDG and PC algorithms for nodes involved in unshielded collider structures and all other remaining patterns pooled together. In supplemental Figures S2 and S3 we highlighted all nodes involved in unshielded collider patterns.