stringgaussnet (version 1.1)

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

Description

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

Usage

## S3 method for class 'default':
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)