stringgaussnet (version 1.1)

ShortPathSTRINGNet.default: Function to create object of class ShortPathSTRINGNet

Description

This function is used by getShorthestPaths() to convert results from the computation of shortest paths from STRING network.

Usage

## S3 method for class 'default':
ShortPathSTRINGNet(x, DEGenes, GenesAnnotations = NULL, ...)

Arguments

x

The non-formatted shortest paths STRING network obtained by getShortestPaths.

DEGenes

DE genes analysis results, which are used for primary node attributes.

GenesAnnotations

Gene annotations got by biomaRt if it was requested by getSTRINGNetwork(). 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 distances, intermediate nodes separated by commas, and number of intermediate nodes. - 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

ShortPathSTRINGNet, getShortestPaths, print.ShortPathSTRINGNet, summary.ShortPathSTRINGNet, export.ShortPathSTRINGNet

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)