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-4.5-noble)qtlnet_1.5.4.tar.gz(r-4.4-noble)
qtlnet_1.5.4.tgz(r-4.4-emscripten)qtlnet_1.5.4.tgz(r-4.3-emscripten)
qtlnet.pdf |qtlnet.html✨
qtlnet/json (API)

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

Peer review:

Datasets:

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

2.38 score 12 scripts 204 downloads 2 mentions 29 exports 46 dependencies

Last updated 5 years agofrom:67353cbb52. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 07 2024
R-4.5-linuxOKDec 07 2024

Exports:best.qtlnetbic.joinbic.qtlnetcheck.qtlnetdist.qtlnetedgematch.qtlnetest.qtlnetgenerate.qtl.markersgenerate.qtl.phenograph.qdggraph.qtlnetgroup.qtlnetigraph.qtlnetinit.qtlnetloci.qtlnetmcmc.qtlnetparallel.qtlnetparents.qtlnetplot.qtlnetplotbic.qtlnetprint.qtlnetprint.summary.qtlnetqdgqdg.perm.testqdg.semsize.qtlnetsubset.qtlnetsummary.qtlnetwrite.qtlnet

Dependencies:abindarmbdsmatrixBHBiocGenericsBiocManagerbootcliclueclustercodacolorspacecorpcorcpp11DEoptimRfastICAgenericsggmgluegraphigraphlatticelifecyclelme4lmtestmagrittrMASSMatrixmiminqanlmenloptrpcalgpkgconfigqtlRBGLRcppRcppArmadilloRcppEigenrlangrobustbasesemsfsmiscvcdvctrszoo

QTLNET Overview

Rendered fromqtlnet.Rnwusingutils::Sweaveon Dec 07 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Acyclic graph exampleacyclic acyclic.data acyclic.DG acyclic.qdg acyclic.qtl
Pre-compute BIC values for qtlnet sampling.bic.join bic.qtlnet Pscdbp.bic
Cyclic graph (a) examplecyclica cyclica.data cyclica.qtl
Cyclic graph (b) examplecyclicb cyclicb.data cyclicb.qtl
Cyclic graph (c) examplecyclicc cyclicc.data cyclicc.qtl
QTL network diagnostic routinesdist.qtlnet edgematch.qtlnet mds.qtlnet plotbic.qtlnet
Generate QTLs ane phenotypes from cross objectgenerate.qtl.markers generate.qtl.pheno
Generate and graph Glx networkglxnet glxnet.cross glxnet.qdg glxnet.qtl
qtlnet plot using igraphgraph.qtlnet igraph.qtlnet plot.qtlnet
QTL architecture per node as listest.qtlnet loci.qtlnet
Sample genetic architecture and QTL networkinit.qtlnet mcmc.qtlnet qtlnet
Code to parallelize use of qtlnetparallel.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 algorithmgraph.qdg print.qdg qdg summary.qdg
Conduct permutation test for LOD score of edge direction on directed graphprint.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 tablecheck.qtlnet print.qtlnet print.summary.qtlnet summary.qtlnet
write qtlnet as text filewrite.qtlnet