resampleWGCNA - Resampling-based approaches to weighted gene coexpression analysis results

This package contains two functions which were developed as part an empirical study. If you use any of the functions in the package, kindly cite:

Fruciano C., Meyer A., Franchini P. 2019. Divergent Allometric Trajectories in Gene Expression and Coexpression Produce Species Differences in Sympatrically SpeciatingMidas Cichlid Fish. Genome Biology and Evolution 11(6):1644–1657. doi: 10.1093/gbe/evz108

More specific citation details are provided in the help of each function.

The package currently contains two functions, which perform permutation tests ancillary to a normal WGCNA analysis:

• test_eigengene_explained_variance: performs a permutation test of the variance explained by the "eigengene" of a selected module
• test_RV_target_module: performs a permutation test based on the Escoufier RV coefficient of the multivariate association between the expression of genes in a given module and a univariate or multivariate array (e.g., phenotype)

Installation

From Github, using devtools

library(devtools)
install_github("fruciano/resampleWGCNA")