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Runs WGCNA TOMsimilarity

Source: R/wgcnaTOM.R
wgcnaTOM.Rd

Runs WGCNA::TOMsimilarity over a gene expression matrix.

Usage

wgcnaTOM(
  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 wgcnaTopologicalOverlapMatrixNetwork.csv to `outputpath`