Other packages > Find by keyword >

graphsim  

Simulate Expression Data from 'igraph' Networks
View on CRAN: Click here


Download and install graphsim package within the R console
Install from CRAN:
install.packages("graphsim")

Install from Github:
library("remotes")
install_github("cran/graphsim")

Install by package version:
library("remotes")
install_version("graphsim", "1.0.3")



Attach the package and use:
library("graphsim")
Maintained by
S. Thomas Kelly
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-03-16
Latest Update: 2022-09-12
Description:
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.
How to cite:
S. Thomas Kelly (2020). graphsim: Simulate Expression Data from 'igraph' Networks. R package version 1.0.3, https://cran.r-project.org/web/packages/graphsim. Accessed 21 Nov. 2024.
Previous versions and publish date:
0.1.2 (2020-03-16 15:10), 1.0.0 (2020-07-02 09:40), 1.0.1 (2020-07-17 11:50), 1.0.2 (2021-07-30 10:00)
Other packages that cited graphsim R package
View graphsim citation profile
Other R packages that graphsim depends, imports, suggests or enhances
Complete documentation for graphsim
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
deductive  
Data Correction and Imputation Using Deductive Methods
Attempt to repair inconsistencies and missing values in data records by using information from vali ...
Download / Learn more Package Citations See dependency  
SCBiclust  
Identifies Mean, Variance, and Hierarchically Clustered Biclusters
Identifies a bicluster, a submatrix of the data such that the features and observations within the s ...
Download / Learn more Package Citations See dependency  
pkgdepends  
Package Dependency Resolution and Downloads
Find recursive dependencies of 'R' packages from various sources. Solve the dependencies to obtain ...
Download / Learn more Package Citations See dependency  
RcppHNSW  
'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors
'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This package provides a minimal R int ...
Download / Learn more Package Citations See dependency  
crossrun  
Joint Distribution of Number of Crossings and Longest Run
Joint distribution of number of crossings and the longest run in a series of independent Bernoulli ...
Download / Learn more Package Citations See dependency  

23,229

R Packages

199,929

Dependencies

62,984

Author Associations

23,230

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA