prepDataForIMAT.m

function [model, options] = prepDataForIMAT(startModel, exprData)
%       
%           starModel = a model the expresion to be mapped onto; an example
%                       might be recon RPMI medium simulated
%           exprData  = a file of 2 columns:
%               column 1 should be called 'gene'
%               column 2 should be called 'value'
%                       


% Assign reaction expressions
[expressionRxns, parsedGPR] = mapExpressionToReactions(startModel, exprData);

% Transform the expression
expressionTransformed = zeros(length(expressionRxns), 1);
for n = 1:length(expressionRxns)
    if expressionRxns(n, 1) > 0
        expressionTransformed(n, 1) = log(expressionRxns(n, 1));
    else
        expressionTransformed(n, 1) = expressionRxns(n, 1);
    end
end

% Expression without values that cannot be log-ed
holdExpression    = expressionRxns(expressionRxns > 0);
holdExpressionLog = log(holdExpression);

meanExpression    = mean(holdExpressionLog);
standardDevExpr   = std (holdExpressionLog);

model             = writeCbModel(startModel, 'xls', 'modelRPMIcontrol');

upper = meanExpression + 1/2*(standardDevExpr);
lower = meanExpression - 1/2*(standardDevExpr);

options.solver         = 'iMAT';
options.expressionRxns = expressionTransformed;
options.threshold_lb   = lower;
options.threshold_ub   = upper;
options.runtime        = 259200; %Three days max runtime
end