readSIF: Read a SIF file and create a model object

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

Description

This function reads in a cytoscape SIF file and creates a model object that can be used in the CellNOptR procedure.

Usage

readSIF(sifFile)

Arguments

sifFile

The name of a SIF file (Cytoscape format). See details for the accepted format.

Details

The input argument is the name of a SIF file that contains a prior knowledge network. The SIF format (See http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats/) can be of the form:

nodeA typeA node2

or

node2 typeB node3 node4

with space or tabulations in between types and nodes. Spaces and tabulations have different meaning in the original cytoscape format. However, we do not differentiate them. Therefore names of the nodes cannot have white space inside them.

The accepted values for the types are -1 (inhibitor) or 1 (normal relation).

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.

The SIF format can also include unconnected node that is a row with a single name:

nodeA

Although there would be no error, these type of rows are ignored.

Value

a model list with fields:

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
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
namesSpecies	vector that contains the names of the species in the same order as the rows of the interMat and notMat matrices
reacID	vector that holds character strings specifying the reaction in full letters, in the same order as the columns of interMat and notMat

Author(s)

C. Terfve

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.

Examples

cpfile<-dir(system.file("ToyModel",package="CellNOptR"),full=TRUE)
file.copy(from=cpfile,to=getwd(),overwrite=TRUE)
ToyModel<-readSIF(sifFile="ToyPKNMMB.sif")

CellNOptR documentation built on Nov. 8, 2020, 6:58 p.m.