fit_modules: Perform soft thresholding in preparation for WGCNA module...

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

Perform soft thresholding in preparation for WGCNA module building

Description

Perform soft thresholding in preparation for WGCNA module building

Usage

fit_modules(
  dat,
  genes = NULL,
  powerVector = c(1:30),
  networkType = "signed",
  nThread = 2
)

Arguments

dat	limma EList output by voom( ). Must include dat$E
genes	Character vector of genes to used in module building. Must match rownames in dat. If not set, all genes in dat are used
powerVector	Numeric vector of soft thresholding powers for which the scale free topology fit indices are to be calculated. Default c(1:30)
networkType	Character string of network type. Allowed values are "unsigned", "signed", "signed hybrid"
nThread	Integer for number of threads to use

Value

List including:

• genes Character vector of genes used in module building

• sft Data frame with soft thresholding results including R-squared, slope, and k metrics

• top.plot ggplot object of soft thresholding topology

• connect.plot ggplot object of soft thresholding connectivity

Examples

fit <- fit_modules(dat = example.voom)

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