readSBMLQual: Read a SBMLQual document and returns a SIF object (as...

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

Read a SBMLQual document and returns a SIF object (as returned by readSIG

Description

This function reads a SBMLQual XML file where a model is stored. The XML is scanned and saved in SIF format in a temporary file. This file is read by readSIF. The returned object is therefore the output of readSIF.

Usage

readSBMLQual(filename)

Arguments

filename

The name of a SBMLQual file.

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)

T. Cokelaer

References

SBMLQual: qualitative models. See SBML.org for details.

Examples

## Not run: 
sif = readSBMLQual("test.xml")

## End(Not run)

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