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qtlnet (version 1.5.4)

Causal Inference of QTL Networks

Description

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. .

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Version

Install

install.packages('qtlnet')

Monthly Downloads

184

Version

1.5.4

License

GPL (>= 2)

Maintainer

Brian Yandell

Last Published

April 13th, 2020

Functions in qtlnet (1.5.4)

dist.qtlnet

QTL network diagnostic routines
summary.qtlnet

summary of model average network and posterior table
write.qtlnet

write qtlnet as text file
generate.qtl

Generate QTLs ane phenotypes from cross object
Pscdbp

Cross and qtlnet objects with Ghazalpour et al. (2006) data. Only 13 phenotypes are included.
bic.qtlnet

Pre-compute BIC values for qtlnet sampling.
parallel.qtlnet

Code to parallelize use of qtlnet
qdg.perm.test

Conduct permutation test for LOD score of edge direction on directed graph
cyclica

Cyclic graph (a) example
cyclicc

Cyclic graph (c) example
cyclicb

Cyclic graph (b) example
igraph.qtlnet

qtlnet plot using igraph
glxnet

Generate and graph Glx network
acyclic

Acyclic graph example
loci.qtlnet

QTL architecture per node as list
qdg

Produces a directed graph using QDG algorithm
qdg.sem

Score directed graphs outputed by qdg using structural equation models (SEM)
subset.qtlnet

Catenate or subset qtlnet object(s).
parents.qtlnet

Determine and group node-parent combinations.
mcmc.qtlnet

Sample genetic architecture and QTL network