stringgaussnet (version 1.1)

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

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.

Value

• An object of class ShortPathSTRINGNet.

Details

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

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)