simPATHy: A Method for Simulating Data from Perturbed Biological Pathways
Version 0.2

Simulate data from a Gaussian graphical model or a Gaussian Bayesian network in two conditions. Given a covariance matrix of a reference condition simulate plausible dysregulations.

AuthorElisa Salviato [aut, cre], Vera Djordjilovic [aut], Chiara Romualdi [aut], Monica Chiogna [aut]
Date of publication2016-09-21 07:27:43
MaintainerElisa Salviato <elisa.salviato.88@gmail.com>
LicenseAGPL-3
Version0.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("simPATHy")

Getting started

Vignette simPATHy

Popular man pages

chimera: Chimera data
easyLookDys: Dysregulation summary
easyLookShiny: Visual dysregulation summary
fitSgraph: Estimate covariance matrix of a graphical model
getPathShiny: Choose a path in a graph from an interactive shiny app
makePositiveDefinite: Positive definite matrix
simPATHy: Simulate data from a graphical model
See all...

All man pages Function index File listing

Man pages

chimera: Chimera data
easyLookDys: Dysregulation summary
easyLookShiny: Visual dysregulation summary
fitSgraph: Estimate covariance matrix of a graphical model
generatePath: Find one path in a graph
getPathShiny: Choose a path in a graph from an interactive shiny app
graphNELD3-shiny: Shiny bindings for plotGraphNELD3
makePositiveDefinite: Positive definite matrix
plotCorGraph: Plot correlation or partial correlation matrix
plotGraphNELD3: Dynamic plot of a graph
simPATHy: Simulate data from a graphical model
SMLEdecomposable: Local Maximum Likelihood Estimation

Functions

Dysregulate Source code
SMLEdecomposable Man page Source code
addScaleColor Source code
checkMatrix Source code
chimera Man page
easyLookDys Man page Source code
easyLookShiny Man page Source code
findLeafUg Source code
fitSgraph Man page Source code
generatePath Man page Source code
getBlock Source code
getPathShiny Man page Source code
giveColors Source code
graphNELD3 Source code
graphNELD3-shiny Man page
graphNELD3Output Man page Source code
isNodesConnected Source code
makePositiveDefinite Man page Source code
plotCorGraph Man page Source code
plotGraphNELD3 Man page Source code
plotRect Source code
randomS Source code
renderGraphNELD3 Man page Source code
riscala Source code
simPATHy Man page Source code
uniqueParam Source code

Files

inst
inst/htmlwidgets
inst/htmlwidgets/graphNELD3.js
inst/htmlwidgets/lib
inst/htmlwidgets/lib/d3-3.5.2
inst/htmlwidgets/lib/d3-3.5.2/d3.min.js
inst/htmlwidgets/graphNELD3.yaml
inst/doc
inst/doc/simPATHy.html
inst/doc/simPATHy.Rmd
inst/doc/simPATHy.R
NAMESPACE
data
data/datalist
data/chimera.rda
R
R/graphic_function.R
R/graphNELD3.R
R/main_function.R
R/secondary_function.R
vignettes
vignettes/images
vignettes/images/getPathShiny.png
vignettes/images/easyLookShiny.png
vignettes/images/plotGraphNELD3.png
vignettes/simPATHy.Rmd
vignettes/biblio.bib
MD5
build
build/vignette.rds
DESCRIPTION
man
man/simPATHy.Rd
man/getPathShiny.Rd
man/makePositiveDefinite.Rd
man/plotCorGraph.Rd
man/easyLookShiny.Rd
man/generatePath.Rd
man/graphNELD3-shiny.Rd
man/chimera.Rd
man/easyLookDys.Rd
man/SMLEdecomposable.Rd
man/fitSgraph.Rd
man/plotGraphNELD3.Rd
simPATHy documentation built on May 19, 2017, 6:27 p.m.