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
Use the following code to install the discoMod R package:
# install.packages("devtools")
devtools::install_github("arbet003/discoMod")For a tutorial, see the example near the end of the following help page:
library(discoMod)
?test_modulesWhen 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.