# Causal Inference of QTL Networks

## Documentation for package ‘qtlnet’ version 1.5.4

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

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