getShortestPaths: Get shortest paths between given nodes in STRING network.

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

Description

This function is dedicated to compute shortest paths and to shrink a STRING network between genes selected by the user.

Usage

getShortestPaths(Network, SelectedGenes = 0)

Arguments

Network	Object of class STRINGNet
SelectedGenes	Genes to keep after computation of shortest paths. If equals to 0, initial nodes from DE genes analysis results are selected.

Details

Shortest paths are computed with the Dijkstra's algorithm from the package igraph.

Value

An object of class ShortPathSTRINGNet.

See Also

ShortPathSTRINGNet, ShortPathSTRINGNet.default, print.ShortPathSTRINGNet, summary.ShortPathSTRINGNet, export.ShortPathSTRINGNet, FilterEdges.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)

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