Causal Inference of QTL Networks
Pre-compute BIC values for qtlnet sampling.
QTL network diagnostic routines
Generate QTLs ane phenotypes from cross object
qtlnet plot using igraph
QTL architecture per node as list
Sample genetic architecture and QTL network
Code to parallelize use of qtlnet
Determine and group node-parent combinations.
Conduct permutation test for LOD score of edge direction on directed g...
Produces a directed graph using QDG algorithm
Score directed graphs outputed by qdg using structural equation models...
Catenate or subset qtlnet object(s).
summary of model average network and posterior table
write qtlnet as text file
Functions to Simultaneously Infer Causal Graphs and Genetic Architecture. Includes acyclic and cyclic graphs for data from an experimental cross with a modest number (<10) of phenotypes driven by a few genetic loci (QTL). Chaibub Neto E, Keller MP, Attie AD, Yandell BS (2010) Causal Graphical Models in Systems Genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes. Annals of Applied Statistics 4: 320-339. <doi:10.1214/09-AOAS288>.