make_modules: Construct WGCNA modules and associated data

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

Construct WGCNA modules and associated data

Description

Make WGCNA modules from gene expression data. Also outputs mean or eigenvalue module expression and DAVID formatted gene lists

Usage

make_modules(
  fit,
  Rsq_min = NULL,
  sft_value = NULL,
  minModuleSize = 20,
  maxBlockSize = 500,
  deepSplit = 3,
  networkType = "signed",
  TOMType = "signed",
  mods_mean = FALSE,
  mods_eigen = FALSE,
  david = FALSE,
  nThread = 2,
  Rsq.min = NULL,
  sft.value = NULL,
  mods.mean = FALSE,
  mods.eigen = FALSE
)

Arguments

fit	List object output by fit_modules( )
Rsq_min	Numeric minimum R-squared for soft threshold selection. If set, sft_value is ignored
sft_value	Numeric soft threshold. Set when minimum R-squared is ignored
minModuleSize	Numeric minimum module size. Default is 20
maxBlockSize	Integer giving maximum block size for module detection. Default is 500
deepSplit	Integer value between 0 and 4. Provides a simplified control over how sensitive module detection should be to module splitting, with 0 least and 4 most sensitive
networkType	Character string. Network type. One of "unsigned", "signed", "signed hybrid". Default is "signed"
TOMType	Character string. One of "none", "unsigned", "signed", "signed Nowick", "unsigned 2", "signed 2", or "signed Nowick 2". If "none", adjacency will be used for clustering. See TOMsimilarityFromExpr for details. Default is "signed"
mods_mean	Logical if include mean module expression in output
mods_eigen	Logical if include eigenvalue module expression in output
david	Logical if include DAVID formatted genes in modules in output
nThread	Integer for number of threads to use
Rsq.min	Deprecated form of Rsq_min
sft.value	Deprecated form of sft_value
mods.mean	Deprecated form of mods_mean
mods.eigen	Deprecated form of mods_eigen genes Character vector of genes used in module building sft Data frame with soft thresholding selected for module building. Includes power, minimum R-squared, and connectivity top.plot ggplot object of soft thresholding topology connect.plot ggplot object of soft thresholding connectivity mods Data frame of genes in modules mods.mean Data frame of mean module expression for each library mods.eigen Data frame of module eigenvalue expression for each library david DAVID formatted data frame of genes in modules

Examples

fit <- fit_modules(dat = example.voom)
dat.mods <- make_modules(fit = fit, sft_value = 14,
    mods_mean = TRUE, mods_eigen = TRUE, david = TRUE)

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