stringgaussnet (version 1.1)

SIMoNeNet.default: Function to create object of class SIMoneNet

Description

This function is used by getSIMoNeNet() to convert results from the SIMoNe inference.

Usage

## S3 method for class 'default':
SIMoNeNet(x, DEGeneExpr, GenesAnnotations = NULL, ...)

Arguments

x

The non-formatted SIMoNe network obtained by getSIMoNeNetwork

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 theta scores, 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

SIMoNeNet, getSIMoNeNet, print.SIMoNeNet, summary.SIMoNeNet, export.SIMoNeNet, FilterEdges.SIMoNeNet, pickSIMoNeParam

Examples

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

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

# pickSIMoNeParam(GaussianSpAData)

# GlobalSIMoNeNet<-getSIMoNeNet(GaussianSpAData)
# GlobalSIMoNeNet<-FilterEdges(GlobalSIMoNeNet,0.4)
# print(GlobalSIMoNeNet,5)
# summary(GlobalSIMoNeNet)
# plot(GlobalSIMoNeNet)

# export(GlobalSIMoNeNet,"GlobalSIMoNeNet",T)