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qtlnet (version 1.3.3)
Causal Inference of QTL Networks
Description
Functions to Simultaneously Infer Causal Graphs and Genetic Architecture
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Install
install.packages('qtlnet')
Monthly Downloads
209
Version
1.3.3
License
GPL (>= 2)
Maintainer
Brian S Yandell
Last Published
July 3rd, 2013
Functions in qtlnet (1.3.3)
Search functions
Pscdbp
Cross and qtlnet objects with Ghazalpour et al. (2006) data. Only 13 phenotypes are included.
qdg
Produces a directed graph using QDG algorithm
parents.qtlnet
Determine and group node-parent combinations.
subset.qtlnet
Catenate or subset qtlnet object(s).
igraph.qtlnet
qtlnet plot using igraph
qdg.perm.test
Conduct permutation test for LOD score of edge direction on directed graph
plot.qdg
Plot a directed graph
generate.qtl
Generate QTLs ane phenotypes from cross object
qdg.sem
Score directed graphs outputed by qdg using structural equation models (SEM)
summary.qtlnet
summary of model average network and posterior table
cyclicb
Cyclic graph (b) example
dist.qtlnet
QTL network diagnostic routines
cyclicc
Cyclic graph (c) example
graphviz.qtlnet
qtlnet plot using Rgraphviz
acyclic
Acyclic graph example
bic.qtlnet
Pre-compute BIC values for qtlnet sampling.
loci.qtlnet
QTL architecture per node as list
write.qtlnet
write qtlnet as text file
mcmc.qtlnet
Sample genetic architecture and QTL network
glxnet
Generate and graph Glx network
parallel.qtlnet
Code to parallelize use of qtlnet
cyclica
Cyclic graph (a) example