README.md

In arbet003/discoMod: Identifying differentially co-expressed modules between two groups

discoMod

The goal of discoMod is to identify “modules” (subgroups of correlated genes or other ’omics features), and then test whether the network structure within a module differs between two phenotype groups. By default, the network struture is measured using Spearman’s correlation, but other options are provided. Here is a brief overview of the three main functions:

• find_modules(): model-based clustering to identify modules of correlated genes
• test_modules(): test whether the network structure within a module differs between the two phenotype groups
• corrheatmap(): for a given module, plot correlation heatmaps to visualize differences between the two phenotype groups

Installation

Use the following code to install the discoMod R package:

# install.packages("devtools")
devtools::install_github("arbet003/discoMod")

Tutorial

For a tutorial, see the example near the end of the following help page:

library(discoMod)
?test_modules

Reference

When citing the discoMod R package, please use the following:

Arbet, J., Zhuang, Y., Litkowski, E., Saba, L., & Kechris, K. (2021). Comparing Statistical Tests for Differential Network Analysis of Gene Modules. Frontiers in genetics, 12, 748.

arbet003/discoMod documentation built on Dec. 19, 2021, 4:36 a.m.