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WalhoutLab / MERGE

A new computational pipeline that can be used to convert expression (RNA-seq) data into predicted flux potentials that indicate metabolic function
MIT License
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'boolean' function? #1

Closed kamoors closed 2 years ago

kamoors commented 2 years ago

MATLAB is throwing errors that the function ''boolean'' is undefined, and I could not find it within this repository.

Could you please provide code or explain its purpose?

Thank you in advance!

XuhangLi commented 2 years ago

Hi Kamoors,

It might be a bug related to Matlab version / toolbox dependency. We would like to look into it. Could you please let us know what function gives you the bug? (i.e., xxx.m line xxx)

Thank you very much!

Hang

kamoors commented 2 years ago

Thank you for the super quick reply!

Version: MATLAB R2020b

error:

Undefined function 'boolean' for input arguments of type 'double'.

Error in ExpressionIntegrationByMILP (line 143) OpenGene = HGeneList(boolean(solution.int((2*length(RHindex)+length(RLindex))+1:end)));

Error in IMATplusplus (line 214) [~, ~,~,solution, MILProblem] = ExpressionIntegrationByMILP(worm, RHNames, RLNames,HGenes, epsilon_f, epsilon_r,[],[],verbose);

Error in iMAT_Plus (line 71) = IMATplusplus(model,epsilon_f,epsilon_r, ExpCateg, modelType);

Note: since there are multiple places where the boolean() function is used, there are analogous errors in other places

XuhangLi commented 2 years ago

Thank you for the super quick reply!

Version: MATLAB R2020b

error:

Undefined function 'boolean' for input arguments of type 'double'.

Error in ExpressionIntegrationByMILP (line 143) OpenGene = HGeneList(boolean(solution.int((2*length(RHindex)+length(RLindex))+1:end)));

Error in IMATplusplus (line 214) [~, ~,~,solution, MILProblem] = ExpressionIntegrationByMILP(worm, RHNames, RLNames,HGenes, epsilon_f, epsilon_r,[],[],verbose);

Error in iMAT_Plus (line 71) = IMATplusplus(model,epsilon_f,epsilon_r, ExpCateg, modelType);

Note: since there are multiple places where the boolean() function is used, there are analogous errors in other places

thanks for following up!

The boolean function should be safely replaced by 'logical' if you want to do a quick in-house fix of the bug.

We accidentally have simulink installed in our testing environment so that we have the boolean function. We will update all boolean places soon.

Thank you!

kamoors commented 2 years ago

Thank you! That solved this issue.