| acyclic | Acyclic graph example | 
| acyclic.data | Acyclic graph example | 
| acyclic.DG | Acyclic graph example | 
| acyclic.qdg | Acyclic graph example | 
| acyclic.qtl | Acyclic graph example | 
| best.qtlnet | Catenate or subset qtlnet object(s). | 
| bic.join | Pre-compute BIC values for qtlnet sampling. | 
| bic.qtlnet | Pre-compute BIC values for qtlnet sampling. | 
| c.qtlnet | Catenate or subset qtlnet object(s). | 
| check.qtlnet | summary of model average network and posterior table | 
| cyclica | Cyclic graph (a) example | 
| cyclica.data | Cyclic graph (a) example | 
| cyclica.qtl | Cyclic graph (a) example | 
| cyclicb | Cyclic graph (b) example | 
| cyclicb.data | Cyclic graph (b) example | 
| cyclicb.qtl | Cyclic graph (b) example | 
| cyclicc | Cyclic graph (c) example | 
| cyclicc.data | Cyclic graph (c) example | 
| cyclicc.qtl | Cyclic graph (c) example | 
| dist.qtlnet | QTL network diagnostic routines | 
| edgematch.qtlnet | QTL network diagnostic routines | 
| est.qtlnet | QTL architecture per node as list | 
| generate.qtl.markers | Generate QTLs ane phenotypes from cross object | 
| generate.qtl.pheno | Generate QTLs ane phenotypes from cross object | 
| glxnet | Generate and graph Glx network | 
| glxnet.cross | Generate and graph Glx network | 
| glxnet.qdg | Generate and graph Glx network | 
| glxnet.qtl | Generate and graph Glx network | 
| graph.qdg | Produces a directed graph using QDG algorithm | 
| graph.qtlnet | qtlnet plot using igraph | 
| group.qtlnet | Determine and group node-parent combinations. | 
| igraph.qtlnet | qtlnet plot using igraph | 
| init.qtlnet | Sample genetic architecture and QTL network | 
| loci.qtlnet | QTL architecture per node as list | 
| mcmc.qtlnet | Sample genetic architecture and QTL network | 
| mds.qtlnet | QTL network diagnostic routines | 
| parallel.qtlnet | Code to parallelize use of qtlnet | 
| parents.qtlnet | Determine and group node-parent combinations. | 
| plot.qtlnet | qtlnet plot using igraph | 
| plotbic.qtlnet | QTL network diagnostic routines | 
| print.qdg | Produces a directed graph using QDG algorithm | 
| print.qdg.perm.test | Conduct permutation test for LOD score of edge direction on directed graph | 
| print.qdg.sem | Score directed graphs outputed by qdg using structural equation models (SEM) | 
| print.qtlnet | summary of model average network and posterior table | 
| print.summary.qtlnet | summary of model average network and posterior table | 
| Pscdbp | Cross and qtlnet objects with Ghazalpour et al. (2006) data. Only 13 phenotypes are included. | 
| Pscdbp.bic | Pre-compute BIC values for qtlnet sampling. | 
| Pscdbp.qtlnet | Cross and qtlnet objects with Ghazalpour et al. (2006) data. Only 13 phenotypes are included. | 
| qdg | Produces a directed graph using QDG algorithm | 
| qdg.perm.test | Conduct permutation test for LOD score of edge direction on directed graph | 
| qdg.sem | Score directed graphs outputed by qdg using structural equation models (SEM) | 
| qtlnet | Sample genetic architecture and QTL network | 
| size.qtlnet | Determine and group node-parent combinations. | 
| subset.qtlnet | Catenate or subset qtlnet object(s). | 
| summary.parents.qtlnet | Determine and group node-parent combinations. | 
| summary.qdg | Produces a directed graph using QDG algorithm | 
| summary.qdg.perm.test | Conduct permutation test for LOD score of edge direction on directed graph | 
| summary.qdg.sem | Score directed graphs outputed by qdg using structural equation models (SEM) | 
| summary.qtlnet | summary of model average network and posterior table | 
| write.qtlnet | write qtlnet as text file |