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

Description Usage Arguments Value Author(s) References Examples

View source: R/readSBMLQual.R

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

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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

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

## End(Not run)

CellNOptR documentation built on May 31, 2017, 11:33 a.m.

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