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qtlnet (version 1.2.4)

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

1.2.4

License

GPL (>= 2)

Maintainer

Brian S Yandell

Last Published

June 8th, 2012

Functions in qtlnet (1.2.4)

acyclic

Acyclic graph example

qdg.sem

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

parents.qtlnet

Determine and group node-parent combinations.

loci.qtlnet

QTL architecture per node as list

plot.qdg

Plot a directed graph

parallel.qtlnet

Code to parallelize use of qtlnet

generate.qtl

Generate QTLs ane phenotypes from cross object

qdg

Produces a directed graph using QDG algorithm

glxnet

Generate and graph Glx network

igraph.qtlnet

qtlnet plot using igraph

subset.qtlnet

Catenate or subset qtlnet object(s).

write.qtlnet

write qtlnet as text file

Pscdbp

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

dist.qtlnet

QTL network diagnostic routines

cyclica

Cyclic graph (a) example

bic.qtlnet

Pre-compute BIC values for qtlnet sampling.

cyclicb

Cyclic graph (b) example

qdg.perm.test

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

mcmc.qtlnet

Sample genetic architecture and QTL network

cyclicc

Cyclic graph (c) example

summary.qtlnet

summary of model average network and posterior table

graphviz.qtlnet

qtlnet plot using Rgraphviz