calculate_module_coherence: Calculate WGCNA module coherence

In BIGslu/RNAetc: RNA-seq Data Cleaning And Analysis

Calculate WGCNA module coherence

Description

Calculate within module pairwise gene correlations from WGCNA modules and gene expression data. Test the coherence of modules built from Dataset A in data from Dataset B.

Usage

calculate_module_coherence(
  mods,
  mods_title = "STUDY1",
  mods_var = "module.char",
  remove_mods = c(0, "0", "00", "grey"),
  dat,
  gene_var = "geneName",
  dat_title = "STUDY2",
  return_plot = TRUE,
  r_cutoff = 0.3,
  p_cutoff = 0.01
)

Arguments

mods	Dataframe giving module membership such as output by make_modules. Must include mods_var with module names/IDs and gene_var with gene symbols/IDs
mods_title	Character string specifying name the study/dataset from which modules were built. This is used simply for labeling of outputs. Default = "STUDY1"
mods_var	Character string specifying name of the column in mods df which defines modules. Defaults to "module.char" which is output by make_modules()
remove_mods	Vector of character strings naming modules which you want removed from the analysis. Default includes 0,"0","00","grey"
dat	limma EList output by voom( ) or dataframe contains expression data (like dat$E) in which module coherence is to be tested.
gene_var	Character string specifying name of the column in mods df which gives gene IDs. Values must match rownames in expression data (dat). Defaults to "geneName" which is output by make_modules()
dat_title	Character string specifying name of the study from which the data come. This is used simply for labeling of outputs. Default = "STUDY2"
return_plot	Logical indicating whether plot should be printed when function runs. Defaults = TRUE.
r_cutoff	Vector or single numeric value at which to draw red cutoff lines in correlation plot. Default = 0.3
p_cutoff	Vector or single numeric value at which to draw red cutoff lines in significance plot. Default = 0.01

Value

List including:

• coherence_boxplot_combined A ggplot plot object visualizing distributions of correlation and p values.

• coherence_boxplot_cor A ggplot plot object visualizing distributions of correlation values.

• coherence_boxplot_p A ggplot plot object visualizing distributions of correlation p values.

• subgene_correlation_df Dataframe containing pairwise gene correlations within modules.

• GSabsent A list of missing genes enumerating genes defined in modules but missing from expression data.

#'

Examples

moduleCoherence <- calculate_module_coherence(mods = example.mods,
dat = example.voom, mods_title = "Example WGCNA Modules",
dat_title = "Example Data", r_cutoff = 0.3, p_cutoff = 0.01)

BIGslu/RNAetc documentation built on Feb. 13, 2025, 7:42 a.m.