WGCNA_hubgene: Get top x hub genes for each module.

In Tong-Chen/YSX: For Yishengxin Training

Description

Get top x hub genes for each module.

Usage

WGCNA_hubgene(cyt, top_hub_n = 20, prefix = "ehbio")

Arguments

cyt	A list containing two elements (edgeData and nodeData) generated by WGCNA_cytoscape (specifically onle whithin module interactions are kept in edgeData).
top_hub_n	A number to get top x hub genes.
prefix	prefix for output files.

Value

A dataframe containing selected hub genes.

Examples

df = generateAbundanceDF(nSample=30, nGrp=3, sd=5)
datExpr <- WGCNA_dataFilter(df)
datExpr <- WGCNA_sampleClusterDetectOutlier(datExpr)
power <- WGCNA_softpower(datExpr)
net <- WGCNA_coexprNetwork(datExpr, power)
WGCNA_saveModuleAndMe(net, datExpr)
cyt <- WGCNA_cytoscape(net, power, datExpr)
hubgene <- WGCNA_hubgene(cyt)

#2
exprMat <- "test.file"
wgcnaL <- WGCNA_readindata(exprMat)

traitData <- 'trait.file'
wgcnaL <- WGCNA_readindata(exprMat, traitData)
datExpr <- wgcnaL$datExpr
WGCNA_dataCheck(datExpr)
datExpr <- WGCNA_dataFilter(datExpr)
datExpr <- WGCNA_sampleClusterDetectOutlier(datExpr)
# datExpr <- WGCNA_sampleClusterDetectOutlier(datExpr, traitColors=wgcnaL$traitColors)
power <- WGCNA_softpower(datExpr)
net <- WGCNA_coexprNetwork(datExpr, power)
MEs_col <- WGCNA_saveModuleAndMe(net, datExpr)
WGCNA_MEs_traitCorrelationHeatmap(MEs_col, traitData=wgcnaL$traitData)
cyt <- WGCNA_cytoscape(net, power, datExpr)
hubgene <- WGCNA_hubgene(cyt)

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.