Entropicfba

calculateGeneWeight(model, Transcriptomic, Threshold)[source]

Inputs: model - A COBRA model with mandatory fields: grRules and SConsistentRxnBool. Transcriptomic - A table with entrezID and geneExpression values. Threshold - Threshold for transcriptomic data.

calculateReactionMasses(model)[source]

This function calculates mass related to each reaction, products mass and substrates mass,using the left null space of stochiometric matrix, useful to unbiased flux through reactions with massive metabolites in entropicFBA

plotyy_eFBA(model, objective, C_max, N, d)[source]
This function plot entropicFBA in a plotyy way

Flux through objective function (solution.v)) as a function of C_value on axis1 and and non- linear/ linear/ part of objective function as a function od C_value on axis2 The maximum value of objective function is also plot through FBA

Inputs

  • model – a metabolic model that contain required fields to perform entropicFluxBalanceAnalysis

  • C_max – An estimation for the maximum value of C_value ( for larger number the variables do not change)

  • N – The number of C_value (since the model my be infeasible for some value of C the plotted figure will have fewer numbers in x axis

  • d – a value to set axis in a way that the whole plot is visible