Team:Alberta/Project/Modeling/FindEssentials

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(Difference between revisions)
Line 1: Line 1:
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  %start.m script
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  %Any single gene knockout resulting in less than CutOffCoeff*InitialGrowthRate
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  changeCobraSolver('glpk'); 
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  %will be put into a list
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  model = readCbModel() %('Ec_iAF1260_flux1.xml')
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function [Essentials,grRatio,grRateKO,grRateWT,hasEffect,fluxSolution] = FindEssentials(Model,CutOffCoeff)
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  solution1 = optimizeCbModel(model, 'max', 'false', 'false');
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  Essentials=cell(1);
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  essgenes=cell(1)
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b=1;
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  fValue = solution1.f
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  solution1 = optimizeCbModel(Model, 'max', 'false', 'false');
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  startSays = 'Copy & paste your literature/suspected gene list into essgenes!'
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  InitialGrowthRate = solution1.f; %For clarity
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g=CutOffCoeff*InitialGrowthRate;
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[grRatio,grRateKO,grRateWT,hasEffect,fluxSolution]=singleGeneDeletion(Model);
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%This part uses the results of singleGeneDeletion to make a list
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%containing all of the genes whose deletion caused a growth rate less than
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%g
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for a=(1:length(grRateKO))
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    if grRateKO(a)<g
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        Essentials(b) = Model.genes(a);
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        b=b+1;
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    end
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  end
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NumberOfEssentialGenes = length(Essentials)
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Essentials = Essentials';

Revision as of 06:31, 2 October 2009

%Any single gene knockout resulting in less than CutOffCoeff*InitialGrowthRate
%will be put into a list
function [Essentials,grRatio,grRateKO,grRateWT,hasEffect,fluxSolution] = FindEssentials(Model,CutOffCoeff)
Essentials=cell(1);
b=1;
solution1 = optimizeCbModel(Model, 'max', 'false', 'false');
InitialGrowthRate = solution1.f; %For clarity
g=CutOffCoeff*InitialGrowthRate;
[grRatio,grRateKO,grRateWT,hasEffect,fluxSolution]=singleGeneDeletion(Model);

%This part uses the results of singleGeneDeletion to make a list
%containing all of the genes whose deletion caused a growth rate less than
%g

for a=(1:length(grRateKO))
    if grRateKO(a)<g
        Essentials(b) = Model.genes(a);
        b=b+1;
    end
end

NumberOfEssentialGenes = length(Essentials)
Essentials = Essentials';
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