Type I error and power comparison between causality methods derived from computer simulated F2 mouse crosses. For each autosome of each replicate cross of N = 1000 total crosses, a clinical trait and potential mediating trait were simulated under a variety of true causal scenarios. For each scenario, a wide range of positive and negative effect sizes were randomly selected for each chromosome of each cross. 'Neighbors' denote chromosome-specific QTL peak pairs. Causal models are, causal (C), reactive (R), independent (I), hidden variable affecting both traits (H), and no associations between genotypes and traits (Null). Filtering criteria were applied such that only neighbors where both QTL peaks achieved a p-value of .001 or smaller were tested. For the AIC and BNC methods, a bootstrap consistency of .7 was required to accept the causal call. Note that 'power' is estimated ignoring those gene-trait pairs that did not both meet the p-value significance threshold.
Millstein et al. BMC Genetics 2009 10:23 doi:10.1186/1471-2156-10-23