I need to simulate a eQTL dataset to a given network structure. However, I got quite the difficulties to achieve this. I mean it needs to be identified via MatrixEQTL as a eQTL later on. So lets consider the following network with the following edges: A->B B->C A->C The simulation should now such that each node represents a expression trait for a which a SNP is directly linked to. SNPs should then be significant for each expression trait that is reachable node it is linked to. Lets say the SNP for trait A should be significant to the traits A,B and C and so on. SNPs are binary vectors.
How can I achieve this correlation between SNPs and expression traits? I used the paper from Zhu(2007): "Increasing the Power to Detect Causal Associations by Combining Genotypic and Expression Data in Segregating Populations". However in this settings the SNPs are not taken into account and are assume to be given.
How can I achieve this? I need to do this in R.