wgcnaSoftThreshold: Runs WGCNA

In Sage-Bionetworks/metanetwork: Network meta analysis

Runs WGCNA

Description

Runs WGCNA::pickSoftThreshold over a gene expression matrix.

Usage

wgcnaSoftThreshold(
  data,
  path = NULL,
  pval = 1,
  outputpath,
  RsquaredCut = 0.8,
  defaultNaPower = 6
)

Arguments

data	Required. Gene expression data in a matrix or data frame. Rows correspond to samples and columns to genes.
path	Optional. Not utilized in this function. (Default = NULL)
pval	Optional. Not utilized in this function. (Default = 1)
outputpath	Required. The file path to write the resulting coexpression network.
RsquaredCut	Optional. Desired minimum scale free topology fitting index R^2. (Default = 0.80)
defaultNaPower	Optional. The power to rais the abs(cor(data)) matrix to if thee power estimate from WGCNA::pickSoftThreshold() is too low (Default = 6).

Value

NULL. Writes coexpression network named wgcnaSoftThresholdNetwork.csv to 'outputpath'

Sage-Bionetworks/metanetwork documentation built on April 27, 2022, 7:42 a.m.