qtlnet: Causal Inference of QTL Networks

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Functions to Simultaneously Infer Causal Graphs and Genetic Architecture

Author
Elias Chaibub Neto <echaibub@hotmail.com> and Brian S. yandell <byandell@wisc.edu>
Date of publication
2014-03-14 00:03:29
Maintainer
Brian S. Yandell <byandell@wisc.edu>
License
GPL (>= 2)
Version
1.3.6
URLs

View on CRAN

Man pages

acyclic
Acyclic graph example
bic
Pre-compute BIC values for qtlnet sampling.
cyclica
Cyclic graph (a) example
cyclicb
Cyclic graph (b) example
cyclicc
Cyclic graph (c) example
diag
QTL network diagnostic routines
generate
Generate QTLs ane phenotypes from cross object
glxnet
Generate and graph Glx network
igraph
qtlnet plot using igraph
loci
QTL architecture per node as list
mcmc
Sample genetic architecture and QTL network
parallel
Code to parallelize use of qtlnet
parents
Determine and group node-parent combinations.
Pscdbp
Cross and qtlnet objects with Ghazalpour et al. (2006) data....
qdg
Produces a directed graph using QDG algorithm
qdg.perm.test
Conduct permutation test for LOD score of edge direction on...
sem
Score directed graphs outputed by qdg using structural...
subset
Catenate or subset qtlnet object(s).
summary
summary of model average network and posterior table
write
write qtlnet as text file

Files in this package

qtlnet
qtlnet/inst
qtlnet/inst/parallel
qtlnet/inst/parallel/Phase1.R
qtlnet/inst/parallel/Phase4.R
qtlnet/inst/parallel/params.txt
qtlnet/inst/parallel/Phase3.R
qtlnet/inst/parallel/notes.txt
qtlnet/inst/parallel/Phase2.R
qtlnet/inst/parallel/Phase5.R
qtlnet/inst/graphviz
qtlnet/inst/graphviz/qtlnet.R
qtlnet/inst/graphviz/qdg.R
qtlnet/inst/graphviz/Rgraphviz.R
qtlnet/inst/graphviz/graphviz.Rd
qtlnet/inst/graphviz/plot.qdg.Rd
qtlnet/inst/example
qtlnet/inst/example/notes.txt
qtlnet/inst/example/qdg.txt
qtlnet/inst/example/codetree.txt
qtlnet/inst/doc
qtlnet/inst/doc/qtlnet.pdf
qtlnet/inst/doc/qtlnet.R
qtlnet/inst/doc/qtlnet.Rnw
qtlnet/NAMESPACE
qtlnet/data
qtlnet/data/acyclic.RData
qtlnet/data/Pscdbp.RData
qtlnet/data/Pscdbp.bic.RData
qtlnet/data/glxnet.RData
qtlnet/data/cyclica.RData
qtlnet/data/cyclicb.RData
qtlnet/data/cyclicc.RData
qtlnet/data/datalist
qtlnet/data/Pscdbp.qtlnet.RData
qtlnet/R
qtlnet/R/write.R
qtlnet/R/perm.R
qtlnet/R/scanone.R
qtlnet/R/solution.R
qtlnet/R/parallel.R
qtlnet/R/lod.score.R
qtlnet/R/average.R
qtlnet/R/qdg.R
qtlnet/R/score.R
qtlnet/R/cov.matrix.R
qtlnet/R/generate.R
qtlnet/R/log.like.R
qtlnet/R/diag.R
qtlnet/R/bic.R
qtlnet/R/summary.R
qtlnet/R/mcmc.R
qtlnet/R/sem.R
qtlnet/R/loci.R
qtlnet/R/igraph.R
qtlnet/vignettes
qtlnet/vignettes/qtlnet.Rnw
qtlnet/MD5
qtlnet/build
qtlnet/build/vignette.rds
qtlnet/DESCRIPTION
qtlnet/man
qtlnet/man/diag.Rd
qtlnet/man/igraph.Rd
qtlnet/man/sem.Rd
qtlnet/man/loci.Rd
qtlnet/man/Pscdbp.Rd
qtlnet/man/parallel.Rd
qtlnet/man/glxnet.Rd
qtlnet/man/bic.Rd
qtlnet/man/write.Rd
qtlnet/man/acyclic.Rd
qtlnet/man/parents.Rd
qtlnet/man/cyclicc.Rd
qtlnet/man/cyclica.Rd
qtlnet/man/qdg.Rd
qtlnet/man/generate.Rd
qtlnet/man/qdg.perm.test.Rd
qtlnet/man/cyclicb.Rd
qtlnet/man/subset.Rd
qtlnet/man/summary.Rd
qtlnet/man/mcmc.Rd