stringgaussnet (version 1.1)

WGCNANet.default: Function to create an object of class WGCNANet

Description

This function is used by getWGCNANet() to convert results from the WGCNA inference.

Usage

## S3 method for class 'default':
WGCNANet(x, SoftThreshold, AThreshold, Correlations, PValues, DEGeneExpr,
	GenesAnnotations = NULL, ...)

Arguments

x

Computed adjacency matrix by getWGCNANet()

SoftThreshold

Soft threshold parameter (alpha) used for adjacency computation by sigmoid function

AThreshold

Threshold on adjacency score for edges inference

Correlations

Correlations (spearman's rho) matrix between all pairs of genes

PValues

Spearman's p-value computed between all pairs of genes

DEGeneExpr

DE genes analysis results contained in an object of class DEGeneExpr. Those will be used as primary node attributes.

GenesAnnotations

Gene annotations got by biomaRt if it was requested by getSIMoNeNet(). Those will be used as secondary node attributes.

...

Additional parameters. Not used here.

Value

• A list with at least two data frames: - Edge attributes, with spearman's rhos and p-values. - Node attributes given by DE genes analysis results. A third data frame giving gene annotations can be added if it is not null when calling the function.

See Also

WGCNANet, getWGCNANet, 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"))