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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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Version

Install

install.packages('qtlnet')

Monthly Downloads

219

Version

1.3.3

License

GPL (>= 2)

Maintainer

Brian S Yandell

Last Published

July 3rd, 2013

Functions in qtlnet (1.3.3)

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