graphsim: Simulate Expression Data from 'igraph' Networks

Functions to develop simulated continuous data (e.g., gene expression) from a sigma covariance matrix derived from a graph structure in 'igraph' objects. Intended to extend 'mvtnorm' to take 'igraph' structures rather than sigma matrices as input. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. Here we present a versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from a multivariate normal distribution derived from a graph structure. This package allows the simulation of biological pathways from a graph structure based on a statistical model of gene expression. For example methods to infer biological pathways and gene regulatory networks from gene expression data can be tested on simulated datasets using this framework. This also allows for pathway structures to be considered as a confounding variable when simulating gene expression data to test the performance of genomic analyses.

Version: 1.0.1
Depends: R (≥ 2.10)
Imports: utils, gplots, igraph, mvtnorm, Matrix, matrixcalc, graphics
Suggests: devtools, knitr (≥ 1.5), markdown, prettydoc, R.rsp, rmarkdown, testthat, scales, vdiffr
Published: 2020-07-17
Author: S. Thomas Kelly [ctb], S. Thomas Kelly [aut, cre], Michael A. Black [aut, ths], Robrecht Cannoodt [ctb], Jason Cory Brunson [ctb]
Maintainer: S. Thomas Kelly <tom.kelly at riken.jp>
BugReports: https://github.com/TomKellyGenetics/graphsim/issues/
License: GPL-3
NeedsCompilation: no
Citation: graphsim citation info
Materials: README NEWS
CRAN checks: graphsim results

Downloads:

Reference manual: graphsim.pdf
Vignettes: Directed plots for igraph objects
Simulating network graph structure in continuous data
Package source: graphsim_1.0.1.tar.gz
Windows binaries: r-devel: graphsim_1.0.1.zip, r-release: graphsim_1.0.1.zip, r-oldrel: graphsim_1.0.1.zip
macOS binaries: r-release: graphsim_1.0.1.tgz, r-oldrel: graphsim_1.0.1.tgz
Old sources: graphsim archive

Reverse dependencies:

Reverse suggests: leiden

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