Home > RAVEN > markPathwayWithFluxes.m

markPathwayWithFluxes

PURPOSE ^

markPathwayWithFluxes

SYNOPSIS ^

function [returnPathway errorFlag]= markPathwayWithFluxes(pathway, reactionIDs, fluxes, referenceFluxes)

DESCRIPTION ^

 markPathwayWithFluxes
   Marks each enzyme in a pathway structure with the corresponding fluxes
   from two simulation results. This is done for enzymes that has the name
   of a reaction in the note field. The reaction has to be present in
   reactionIDs.

   pathway         pathway structure of the metabolic network
   reactionsIDs    cell array with the names of the reactions in the model
   fluxes          vector with flux values
   referenceFluxes vector with fluxes to compare to

   returnPathway   updates the original pathway structure by adding the
                   fields flux and referenceFlux for each marked reaction
   errorFlag       true if there has been an error

   Usage: [returnPathway errorFlag] = markPathwayWithFluxes(pathway, reactionIDs,
   fluxes, referenceFluxes)

   Rasmus Agren, 2010-12-16

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [returnPathway errorFlag]= markPathwayWithFluxes(pathway, reactionIDs, fluxes, referenceFluxes)
0002 % markPathwayWithFluxes
0003 %   Marks each enzyme in a pathway structure with the corresponding fluxes
0004 %   from two simulation results. This is done for enzymes that has the name
0005 %   of a reaction in the note field. The reaction has to be present in
0006 %   reactionIDs.
0007 %
0008 %   pathway         pathway structure of the metabolic network
0009 %   reactionsIDs    cell array with the names of the reactions in the model
0010 %   fluxes          vector with flux values
0011 %   referenceFluxes vector with fluxes to compare to
0012 %
0013 %   returnPathway   updates the original pathway structure by adding the
0014 %                   fields flux and referenceFlux for each marked reaction
0015 %   errorFlag       true if there has been an error
0016 %
0017 %   Usage: [returnPathway errorFlag] = markPathwayWithFluxes(pathway, reactionIDs,
0018 %   fluxes, referenceFluxes)
0019 %
0020 %   Rasmus Agren, 2010-12-16
0021 %
0022 
0023 %Check if all variables are of the correct dimension
0024 if length(reactionIDs)~=length(fluxes) || length(reactionIDs)~=length(referenceFluxes)
0025     returnPathway=pathway;
0026     errorFlag=1;
0027     fprintf('reactionIDs, fluxes, and referenceFluxes do not have the same number of elements.');
0028     return;
0029 end
0030 
0031 %Loop through the components in the pathway. Check if any component has a
0032 %note and then check for the corresponding reaction id
0033 returnPathway=pathway;
0034 
0035 for i=1:length(pathway.listOfSpecies)
0036    if strcmpi(pathway.listOfSpecies(i).type,'PROTEIN')
0037       if isfield(pathway.listOfSpecies(i),'note')
0038           if ~isempty(pathway.listOfSpecies(i).note)
0039              %If there is a note check if there is a corresponding reaction id
0040              index=find(strcmpi(reactionIDs,pathway.listOfSpecies(i).note));
0041              %If there is a match
0042              if any(index)
0043                  returnPathway.listOfSpecies(i).flux=fluxes(index);
0044                  returnPathway.listOfSpecies(i).referenceFlux=referenceFluxes(index);
0045              end
0046           end
0047       end
0048    end
0049 end

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