WgcnaClass: create R6 class method for WGCNA

In hcnh174/hlsgr: Hiroshima Liver Study Group R Utilities

create R6 class method for WGCNA

Description

create R6 class method for WGCNA

create R6 class method for WGCNA

Methods

Public methods

• WgcnaClass$new()

• WgcnaClass$plotSampleTree()

• WgcnaClass$cutoffline()

• WgcnaClass$cutTreeStatic()

• WgcnaClass$cutTreeDynamic()

• WgcnaClass$plotDendogram()

• WgcnaClass$pickSoftThreshold()

• WgcnaClass$plotSoftThreshold()

• WgcnaClass$plotMeanConnectivity()

• WgcnaClass$constructNetwork()

• WgcnaClass$plotDendogramWithColors()

• WgcnaClass$plotTomPlot()

• WgcnaClass$plotModuleTraitRelationship()

• WgcnaClass$selectHubs()

• WgcnaClass$goEnrichmentAnalysis()

• WgcnaClass$exportCytoscape()

• WgcnaClass$clone()

---

Method new()

Usage

WgcnaClass$new(rnaseq, datTraits, identifier = "ensembl_id")

Arguments

datTraits

---

Method plotSampleTree()

Usage

WgcnaClass$plotSampleTree()

---

Method cutoffline()

Usage

WgcnaClass$cutoffline()

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Method cutTreeStatic()

Usage

WgcnaClass$cutTreeStatic()

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Method cutTreeDynamic()

Usage

WgcnaClass$cutTreeDynamic(deepSplit = 2)

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Method plotDendogram()

Usage

WgcnaClass$plotDendogram(signed = FALSE)

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Method pickSoftThreshold()

Usage

WgcnaClass$pickSoftThreshold()

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Method plotSoftThreshold()

Usage

WgcnaClass$plotSoftThreshold()

---

Method plotMeanConnectivity()

Usage

WgcnaClass$plotMeanConnectivity()

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Method constructNetwork()

Usage

WgcnaClass$constructNetwork(
  minModuleSize = 30,
  maxBlockSize = 5000,
  mergeCutHeight = 0.25,
  TOMType = "unsigned"
)

---

Method plotDendogramWithColors()

Usage

WgcnaClass$plotDendogramWithColors()

---

Method plotTomPlot()

Usage

WgcnaClass$plotTomPlot()

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Method plotModuleTraitRelationship()

Usage

WgcnaClass$plotModuleTraitRelationship()

---

Method selectHubs()

Usage

WgcnaClass$selectHubs()

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Method goEnrichmentAnalysis()

Usage

WgcnaClass$goEnrichmentAnalysis()

---

Method exportCytoscape()

Usage

WgcnaClass$exportCytoscape(threshold = 0.02)

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Method clone()

The objects of this class are cloneable with this method.

Usage

WgcnaClass$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

wgcna <- WgcnaClass$new(result, datTraits)

hcnh174/hlsgr documentation built on April 7, 2023, 4:02 p.m.