runWGCNA: WGCNA, Weighted correlation network analysis

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

WGCNA, Weighted correlation network analysis

Description

WGCNA, Weighted correlation network analysis

Usage

runWGCNA(
  datExpr,
  datTraits,
  traitColumnIndex = 1,
  power = NULL,
  minModuleSize = 30,
  MEDissThres = 0.25,
  nSelectHeatmap = 10000
)

Arguments

datExpr	row is sample
datTraits	0 1 to indicate group. Numeric to indicate trait
traitColumnIndex	Trait we are interested in
power	Default by sft$powerEstimate
minModuleSize	We like large modules, so we set the minimum module size relatively high:
MEDissThres	We choose a height cut of 0.25, corresponding to correlation of 0.75, to merge
nSelectHeatmap	n (default 1000) genes to show in heatmap (a way to visualize network)

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.