Convert a model object in sif format

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Description

This function receives as input a model object and converts it to the cytoscape sif format. It can be used to convert either the whole model (before or after pre-processing) or the optimized one (if the corresponding bitString in provided). The resulting table can also be saved in a sif file.

Usage

1
model2sif(model,optimRes=NA,writeSif=FALSE, filename="Model")

Arguments

model

the model as generated using readSIF

optimRes

the output of the optimisation (as obtained using gaBinaryT1), default set to NA the whole model in converted

writeSif

it 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

All links in the model are converted in sif format that is sourceNode-tab-sign-tab-targetNode. If there are ANDs, they are converted using dummy nodes called and# (e.g. A+B=C will be A-tab-1-tab-and1; B-tab-1-tab-and1; and1-tab-1-tab-C).

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

graph2sif, sif2graph, readSIF,

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