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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. Intended to extend mvtnorm to take iGraph structures rather than sigma matrices as input.

Installation

To get the dependency package from CRAN:

install.packages(c("igraph", "Matrix", "mvtnorm", "matrixcalc"))

To install the stable release of this package from github:

# install.packages("devtools")
devtools::install_github("TomKellyGenetics/graphsim", ref = "master")

To get the development version of this package from github:

# install.packages("devtools")
devtools::install_github("TomKellyGenetics/graphsim", ref = "dev")

Usage

Please see the vignettes for demonstrations of this package on examples of simple simulated networks and the reactome pathway TGF-β receptor signaling activates SMADs (R-HSA-2173789). A manuscript with further details has been submitted for peer-review.

Citation

To cite the graphsim package in publications use:

S. Thomas Kelly and Michael A. Black (2020). graphsim: Simulate Expression data from iGraph networks R package version 0.1.1. https://github.com/TomKellyGenetics/vioplot doi:10.5281/zenodo.1313986

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {{graphsim}: Simulate Expression data from {iGraph} networks},
    author = {S. Thomas Kelly and Michael A. Black},
    year = {2020},
    note = {R package version 0.1.1},
    url = {https://github.com/TomKellyGenetics/graphsim},
    doi = {10.5281/zenodo.1313986},
  }

Please also acknowledge the manuscript describing use of this package once it is published. It is current avaliable as a preprint.

@article {Kelly2020.03.02.972471,
    author = {Kelly, S Thomas and Black, Michael A},
    title = {graphsim: An R package for simulating gene expression data from graph structures of biological pathways},
    elocation-id = {2020.03.02.972471},
    year = {2020},
    doi = {10.1101/2020.03.02.972471},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2020/03/04/2020.03.02.972471},
    eprint = {https://www.biorxiv.org/content/early/2020/03/04/2020.03.02.972471.full.pdf},
    journal = {bioRxiv}
}