compare_modules: Compare WGCNA module builds

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

Compare WGCNA module builds

Description

Make WGCNA modules from gene expression data with dynamic soft threshold selection. Also outputs mean module expression and DAVID formatted gene lists

Usage

compare_modules(
  fit,
  Rsq_min = NULL,
  sft_value = NULL,
  minModuleSize = 20,
  maxBlockSize = 500,
  deepSplit = 3,
  networkType = "signed",
  TOMType = "signed",
  nThread = 2,
  Rsq.min = NULL,
  sft.value = NULL
)

Arguments

fit	List object output by fit_modules( )
Rsq_min	Numeric vector minimum R-squared for soft threshold selection. If set, sft_value is ignored
sft_value	Integer vector soft threshold. Set when minimum R-squared is ignored
minModuleSize	Numeric vector minimum module size. Default is 20
maxBlockSize	Integer vector giving maximum block size for module detection. Default is 500
deepSplit	Integer vector 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 vector. Network type from "unsigned", "signed", "signed hybrid". Default is "signed"
TOMType	Character vector from "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"
nThread	Integer for number of threads to use
Rsq.min	Deprecated form of Rsq_min
sft.value	Deprecated form of sft_value

Value

List including:

• summary Data frame with total modules and sizes for all builds

• modules List of data frames with module sizes for each build

#'

Examples

fit <- fit_modules(dat = example.voom)
compare.mods <- compare_modules(fit = fit, sft_value = c(14, 20))

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