graph2sif: Convert graph to SIF

In saezlab/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Convert graph to SIF

Description

This function converts a network form graph format to SIF format. The resulting table can also be saved in a SIF file.

Usage

graph2sif(graph, writeSif=FALSE, filename="Graph")

Arguments

graph	a graph, as generated using sif2graph
writeSif	if writeSif=FALSE (default) the SIF file is not saved. If writeSif=TRUE it is saved.
filename	the name of the SIF file saved if writeSif=TRUE. Default is Model.sif.

Details

The sign of link is supposed to be encoded in the graph as the weigth of the edge (-1 negative regulation, +1 positive regulation).

Value

sifFile

a table with all the links in the model in the format sourceNode-tab-sign-tab-targetNode

Author(s)

F. Eduati

See Also

model2sif, sif2graph, readSIF,

Examples

    
    data(ToyModel,package="CellNOptR")
    sif_file = tempfile(fileext = ".sif")
    writeSIF(model = ToyModel,filename = sif_file)
    g = sif2graph(sif_file)
    
    graph2sif(graph = g,writeSif = FALSE)
    

saezlab/CellNOptR documentation built on April 16, 2024, 5:21 a.m.