\name{readSif}
\alias{readSif}
\title{
Read a sif file and create a model object
}
\description{
This function reads in a cityscape sif file and creates a model object that can be used in the CellNOptR procedure.
}
\usage{
readSif(sifFile)
}
\arguments{
  \item{sifFile}{
the name of a sif file
}
}
\details{
This function takes in a single argument, sifFile, that points to a previous
knowledge network in .sif format i.e. sourceNode-tab-sign-tab-targetNode. If
there are ANDs they should be introduced as dummy nodes called and# (don't
forget the number after "and" otherwise this won't be recognised).  Please be
aware that "and" nodes are not expected to be negated, i.e. there are not
supposed to be !and1=xyz because that amounts to inverting the sign of all
inputs of and1, which is more simply done at the inputs level.
}
\value{
a model list with fields:
    \item{interMat}{contains a matrix with column for each reaction and a row for each species, with a -1 where the species is the source node and a +1 where the species is a target node, and 0 otherwise}
    \item{notMat}{has the same format as interMat but just contains a 1 if the source node enters the reac with a negative effect, and 0 otherwise}
    \item{namesSpecies}{vector that contains the names of the species in the same order as the rows of the interMat and notMat matrices}
    \item{reacID}{vector that holds character strings specifying the reaction in full letters, in the same order as the columns of interMat and notMat}
}

\references{
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski
B, Ideker T. Cytoscape: a software environment for integrated models of
biomolecular interaction networks. Genome Research 2003 Nov; 13(11):2498-504.
}
\author{
C. Terfve
}
\examples{
tmpdir<-tempdir()
setwd(tmpdir)
cpfile<-dir(system.file("ToyModel",package="CellNOptR"),full=TRUE)
file.copy(from=cpfile,to=getwd(),overwrite=TRUE)
ToyModel<-readSif(sifFile="ToyPKNMMB.sif")
}