SIMoNeNet.default: Function to create object of class SIMoneNet

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

Description

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

Usage

## Default S3 method:
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)

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