CRAN/E | graphsim

graphsim

Simulate Expression Data from 'igraph' Networks

Installation

About

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.

Citation graphsim citation info
github.com/TomKellyGenetics/graphsim/
Bug report File report

Key Metrics

Version 1.0.3
R ≥ 2.10
Published 2022-09-12 563 days ago
Needs compilation? no
License GPL-3
CRAN checks graphsim results

Downloads

Yesterday 23 +156%
Last 7 days 97 -14%
Last 30 days 520 -1%
Last 90 days 4.942 +267%
Last 365 days 8.837 +69%

Maintainer

Maintainer

S. Thomas Kelly

tomkellygenetics@gmail.com

Authors

S. Thomas Kelly

aut / cre

Michael A. Black

aut / ths

Robrecht Cannoodt

ctb

Jason Cory Brunson

ctb

Material

README
NEWS
Reference manual
Package source

Vignettes

Simulating network graph structure in continuous data

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

graphsim archive

Depends

R ≥ 2.10

Imports

gplots
igraph
mvtnorm
matrixcalc
Matrix
graphics

Suggests

devtools
knitr ≥ 1.5
markdown
prettydoc
R.rsp
rmarkdown
testthat
scales
vdiffr

Reverse Suggests

leiden