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

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

Description

This function allows to create an object of class MultiNetworks from an object of class MultiDEGeneExpr. This is a wrapper of all methods available in the stringgaussnet package.

Usage

## Default S3 method:
MultiNetworks(x, Methods = c("STRING", "SIMoNe", "WGCNA"), STRINGOptions = NULL,
	SIMoNeOptions = NULL, WGCNAOptions = NULL, SelectInteractionsSTRING = NULL,
	STRINGThreshold = 0, FilterShortPathOptions = NULL, FilterSIMoNeOptions = NULL,
	Factors = NULL, ...)

Arguments

x	An object of class MultiDEGeneExpr
Methods	A character vector indicating which network construction methods to use, among "STRING", "SIMoNe" and "WGCNA"
STRINGOptions	List with parameters available in the function getSTRINGNet()
SIMoNeOptions	List with parameters available in the function getSIMoNeNet()
WGCNAOptions	List with parameters available in the function getWGCNANet()
SelectInteractionsSTRING	A character vector indicating which interaction sources to select in STRINGNet. Please see selectInteractionTypes() for more details.
STRINGThreshold	Confidence score threshold for edge filtering in STRINGNet
FilterShortPathOptions	List with parameters available in the function FilterEdges.ShortPathSTRINGNet()
FilterSIMoNeOptions	List with parameters available in the function FIlterEdges.SIMoNeNet()
Factors	A vector of factors attributed to samples. Must gather all samples present in x.
...	Additional parameters. Not used here.

Value

An object of class MultiNetworks, which is a list of different network objects. If STRING method is used, shortest paths between initial nodes are computed.

See Also

MultiNetworks, print.MultiNetworks, MultiDEGeneExpr.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,])

# MultiSpAData<-MultiDEGeneExpr(GaussianSpAData,DEGeneExpr(t(SpADataExpression[18:34,]),
#	SpADEGenes[18:34,]),DEGeneExpr(t(SpADataExpression[35:51,]),SpADEGenes[35:51,]))
# MultiSpANetworks<-MultiNetworks(MultiSpAData,
#	SelectInteractionsSTRING=c("coexpression","experimental","knowledge"),STRINGThreshold=0.9,
#	FilterSIMoNeOptions=list(Threshold=0.4),Factors=StatusFactor,
#	STRINGOptions=list(AddAnnotations=FALSE),SIMoNeOptions=list(AddAnnotations=FALSE),
#	WGCNAOptions=list(AddAnnotations=FALSE))

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