source("http://bioconductor.org/biocLite.R")
biocLite("ddgraph")

ddgraph

Distinguish direct and indirect interactions with Graphical Modelling

Bioconductor version: 2.13

Distinguish direct from indirect interactions in gene regulation and infer combinatorial code from highly correlated variables such as transcription factor binding profiles. The package implements the Neighbourhood Consistent PC algorithm (NCPC) and draws Direct Dependence Graphs to represent dependence structure around a target variable. The package also provides a unified interface to other Graphical Modelling (Bayesian Network) packages for distinguishing direct and indirect interactions.

Author: Robert Stojnic

Maintainer: Robert Stojnic <robert.stojnic at gmail.com>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("ddgraph")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ddgraph")

 

PDF		ddgraph-cluster.pdf
PDF		ddgraph-ddgraph-plot.pdf
PDF	R Script	Overview of the 'ddgraph' package
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bioinformatics, GraphsAndNetworks, Software
Version	1.6.3
In Bioconductor since	BioC 2.11 (R-2.15)
License	GPL-3
Depends	graph, methods, Rcpp
Imports	bnlearn (>= 2.8), gtools, pcalg, RColorBrewer, plotrix, MASS, Rcpp
Suggests	testthat, Rgraphviz, e1071, ROCR, testthat
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	ddgraph_1.6.3.tar.gz
Windows Binary	ddgraph_1.6.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	ddgraph_1.6.3.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats