Causal Inference of QTL Networks

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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