getWGCNANet: Infer WGCNA network from expression data

In stringgaussnet: PPI and Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor

Description

This function infers a WGCNA network from expression data. This gives a gaussian network simply by filtering on correlations between expressions of each pair of genes. Dissimilarities and modules computations are not implemented, because the main purpose is to compare with SIMoNe results.

Usage

getWGCNANet(DEGeneExpr, SoftThreshold = 8, AThreshold = 0.85, AddAnnotations = F,
	MartDataset = "hsapiens_gene_ensembl")

Arguments

DEGeneExpr	Object of class DEGeneExpr. See DEGeneExpr.default() for more details.
SoftThreshold	Soft threshold parameter (alpha) used for adjacency computation by sigmoid function. See pickWGCNAParam() for some help.
AThreshold	Threshold on adjacency score for edges inference. Generally it is 0.85.
AddAnnotations	Boolean variable indicating whether gene annotations must be added through biomaRt
MartDataset	Which mart dataset to use for querying gene annotations through biomaRt. See getMartDatasets() for some help.

Value

An object of class WGCNANet. See WGCNANet.default() for more details.

See Also

WGCNANet, WGCNANet.default, print.WGCNANet, summary.WGCNANet, export.WGCNANet, pickWGCNAParam, compareGaussNetworks

Examples

# data(SpADataExpression)
# data(SpADEGenes)
# SpAData<-DEGeneExpr(t(SpADataExpression),SpADEGenes)

# NodesForSIMoNe<-rownames(SpADEGenes)[1:17]
# GaussianSpAData<-DEGeneExpr(t(SpADataExpression[NodesForSIMoNe,]),SpADEGenes[NodesForSIMoNe,])

# pickWGCNAParam(GaussianSpAData)
# GlobalWGCNANet<-getWGCNANet(GaussianSpAData)
# print(GlobalWGCNANet,5)
# summary(GlobalWGCNANet)
# plot(GlobalWGCNANet)
# export(GlobalWGCNANet,"GlobalWGCNANet",T)

# compareGaussNetworks(GlobalSIMoNeNet,GlobalWGCNANet,c("SIMoNe","WGCNA"))

stringgaussnet documentation built on May 29, 2017, 10:50 a.m.