compareFactorNetworks: Compare levels of FactorNetworks

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

Description

This function draws a series of plots to compare different levels of a factor used to infer multiple gaussian networks, with an object of class FactorNetworks.

Usage

compareFactorNetworks(Networks, Colors = rainbow(length(Networks)), interactiveMode = T)

Arguments

Networks	An object of class FactorNetworks
Colors	Colors to plot for each level of factor
interactiveMode	Boolean variable indicating whether the plots are in interactive mode. If false, it is useful for automatically saving plots in a single pdf file.

Details

The first plot shows the absolute values of spearman's rho in the different level groups. The second one shows p-values in those different groups. The third displays the respective numbers of edges. The last one shows node connectivities.

See Also

FactorNetworks.default

Examples

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

# StatusFactor<-paste(SpASamples$status,SpASamples$b27,sep=".")
# names(StatusFactor)=SpASamples$chipnum

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

# GlobalSIMoNeNetNF<-getSIMoNeNet(GaussianSpAData)
# GlobalSIMoNeNet<-FilterEdges(GlobalSIMoNeNetNF,0.4)

# StatusFactorSIMoNeNet<-FactorNetworks(GaussianSpAData,StatusFactor,"SIMoNe")
# StatusFactorSIMoNeNet<-FilterEdges(StatusFactorSIMoNeNet,0.4)
# compareFactorNetworks(StatusFactorSIMoNeNet)

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