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

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

Description

This function is used by getSTRINGNet() to convert results from the STRING API into object of class STRINGNet.

Usage

## Default S3 method:
STRINGNet(x, DEGeneExpr, GenesAnnotations = NULL, ...)

Arguments

x	The non-formatted STRING network obtained by getSTRINGNet.
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 getSTRINGNet(). 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 confidence scores given by STRING and multiple edges. - 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

STRINGNet, getSTRINGNet, print.STRINGNet, summary.STRINGNet, export.STRINGNet

Examples

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

# SpASTRINGNet<-getSTRINGNet(SpAData)
# Can be longer.

# SpASTRINGNet<-getSTRINGNet(SpAData,AddAnnotations=FALSE)
# print(SpASTRINGNet,5)
# summary(SpASTRINGNet)
# PPISpASTRINGNet<-selectInteractionTypes(SpASTRINGNet,
#	c("coexpression","experimental","knowledge"),0.9)

# shortPathSpANet<-getShortestPaths(PPISpASTRINGNet)
# shortPathSpANet<-FilterEdges(shortPathSpANet,2.2)
# print(shortPathSpANet,5)
# summary(shortPathSpANet)

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