Package: qtlnet 1.5.4

Brian S. Yandell

qtlnet: Causal Inference of QTL Networks

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. <doi:10.1214/09-AOAS288>.

Authors:Elias Chaibub Neto <[email protected]> and Brian S. yandell <[email protected]>

qtlnet_1.5.4.tar.gz
qtlnet_1.5.4.tar.gz(r-4.7-any)qtlnet_1.5.4.tar.gz(r-4.6-any)
qtlnet_1.5.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
qtlnet/json (API)

# Install 'qtlnet' in R:

install.packages('qtlnet', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

acyclic.data - Acyclic graph example
acyclic.DG - Acyclic graph example
acyclic.qdg - Acyclic graph example
acyclic.qtl - Acyclic graph example
cyclica.data - Cyclic graph (a) example
cyclica.qtl - Cyclic graph (a) example
cyclicb.data - Cyclic graph (b) example
cyclicb.qtl - Cyclic graph (b) example
cyclicc.data - Cyclic graph (c) example
cyclicc.qtl - Cyclic graph (c) example
glxnet.cross - Generate and graph Glx network
glxnet.qdg - Generate and graph Glx network
glxnet.qtl - Generate and graph Glx network
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.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.58 score 19 scripts 354 downloads 2 mentions 29 exports 49 dependencies

Last updated from:67353cbb52. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	191
source / vignettes	OK	238
linux-release-x86_64	OK	205
wasm-release	OK	140

Exports:best.qtlnet bic.join bic.qtlnet check.qtlnet dist.qtlnet edgematch.qtlnet est.qtlnet generate.qtl.markers generate.qtl.pheno graph.qdg graph.qtlnet group.qtlnet igraph.qtlnet init.qtlnet loci.qtlnet mcmc.qtlnet parallel.qtlnet parents.qtlnet plot.qtlnet plotbic.qtlnet print.qtlnet print.summary.qtlnet qdg qdg.perm.test qdg.sem size.qtlnet subset.qtlnet summary.qtlnet write.qtlnet

Dependencies:abind arm bdsmatrix BH BiocGenerics BiocManager boot cli clue cluster coda colorspace corpcor cpp11 DEoptimR fastICA generics ggm glue graph igraph lattice lifecycle lme4 lmtest magrittr MASS Matrix mi minqa nlme nloptr pcalg pkgconfig qtl RBGL rbibutils Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang robustbase sem sfsmisc vcd vctrs zoo

QTLNET Overview

Rendered fromqtlnet.Rnwusingutils::Sweave

Last update: 2020-04-13
Started: 2012-06-08

Help page	Topics
Acyclic graph example	acyclic acyclic.data acyclic.DG acyclic.qdg acyclic.qtl
Pre-compute BIC values for qtlnet sampling.	bic.join bic.qtlnet Pscdbp.bic
Cyclic graph (a) example	cyclica cyclica.data cyclica.qtl
Cyclic graph (b) example	cyclicb cyclicb.data cyclicb.qtl
Cyclic graph (c) example	cyclicc cyclicc.data cyclicc.qtl
QTL network diagnostic routines	dist.qtlnet edgematch.qtlnet mds.qtlnet plotbic.qtlnet
Generate QTLs ane phenotypes from cross object	generate.qtl.markers generate.qtl.pheno
Generate and graph Glx network	glxnet glxnet.cross glxnet.qdg glxnet.qtl
qtlnet plot using igraph	graph.qtlnet igraph.qtlnet plot.qtlnet
QTL architecture per node as list	est.qtlnet loci.qtlnet
Sample genetic architecture and QTL network	init.qtlnet mcmc.qtlnet qtlnet
Code to parallelize use of qtlnet	parallel.qtlnet
Determine and group node-parent combinations.	group.qtlnet parents.qtlnet size.qtlnet summary.parents.qtlnet
Cross and qtlnet objects with Ghazalpour et al. (2006) data. Only 13 phenotypes are included.	Pscdbp Pscdbp.qtlnet
Produces a directed graph using QDG algorithm	graph.qdg print.qdg qdg summary.qdg
Conduct permutation test for LOD score of edge direction on directed graph	print.qdg.perm.test qdg.perm.test summary.qdg.perm.test
Score directed graphs outputed by qdg using structural equation models (SEM)	print.qdg.sem qdg.sem summary.qdg.sem
Catenate or subset qtlnet object(s).	best.qtlnet c.qtlnet subset.qtlnet
summary of model average network and posterior table	check.qtlnet print.qtlnet print.summary.qtlnet summary.qtlnet
write qtlnet as text file	write.qtlnet

Package: qtlnet 1.5.4

qtlnet: Causal Inference of QTL Networks

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)