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Comparison

MATLAB functions in RAVEN/comparison of the RAVEN toolbox. Help text is collected from the source of the tracked branch.

Functions

Function Summary
compareMultipleModels Compare two or more condition-specific models.
compareRxnsGenesMetsComps Compare overlap of genes, reactions, metabolites and compartments.

Reference

compareMultipleModels

Compare two or more condition-specific models.

Compares two or more condition-specific models generated from the same base model using high-dimensional comparisons in the reaction-space.

Input arguments:

Name Type Description Default
models cell

cell array of two or more models.

 required

Name-value arguments:

Name Type Description Default
printResults logical

true if the results should be printed on the screen (default false).
plotResults logical

true if the results should be plotted (default false).
groupVector double or cell

numeric vector or cell array for grouping similar models, i.e. by tissue (default all models ungrouped).
funcCompare logical

should a functional comparison be run (default false).
taskFile char

string containing the name of the task file to use for the functional comparison (should be an .xls or .xlsx file, required for functional comparison).

Output arguments:

Name Type Description
compStruct struct

structure that contains the comparison results, with fields:

  • modelIDs : cell array of model ids
  • reactions : substructure containing reaction information, with fields matrix (binary matrix composed of reactions (rows) in each model (column), used as the input for the model comparisons) and IDs (list of the reactions contained in the reaction matrix)
  • subsystems : substructure containing subsystem information, with fields matrix (matrix with comparison of number of rxns per subsystem) and ID (vector consisting of names of all subsystems)
  • structComp : matrix with pairwise comparisons of model structure based on (1-Hamming distance) between models
  • structCompMap : matrix with 3D tSNE (or MDS) mapping of model structures based on Hamming distances
  • funcComp : substructure containing function comparison results, with fields matrix (matrix with PASS / FAIL (1 / 0) values for each task) and tasks (vector containing names of all tasks)

Examples:

compStruct = compareMultipleModels(models, printResults, ...
    plotResults, groupVector, funcCompare, taskFile);

compareRxnsGenesMetsComps

Compare overlap of genes, reactions, metabolites and compartments.

Compares two or more models with respect to overlap in terms of genes, reactions, metabolites and compartments.

Input arguments:

Name Type Description Default
models cell

cell array of two or more models.

 required

Name-value arguments:

Name Type Description Default
printResults logical

true if the results should be printed on the screen (default false).

Output arguments:

Name Type Description
compStruct struct

structure that contains the comparison, with fields:

  • modelIDs : cell array of model ids

  • rxns, mets, genes, eccodes, metNames, equ, uEqu : the comparison for each field. "equ" are the equations after sorting and "uEqu" are the equations when not taking compartmentalization into account. Each of these contains the sub-fields:

    • comparison : binary matrix where each row indicates which models are included in the comparison
    • nElements : vector with the number of elements for each comparison

Examples:

compStruct = compareRxnsGenesMetsComps(models, printResults);