Newt

writeNewtExperiment(model, metData, metSampleNames, fileName, param)[source]

Writes out an experimental data file for a model exported to SBML and imported into newteditor

USAGE:

writeNewtExperiment (model, metData, metSampleNames, fileName, param)

INPUTS:

  • model – COBRA model structure with fields:

    • .S - m x n stoichiometric matrix

    • .mets - m x 1 array of metabolite identifiers

    • .metNames - m x 1 array of metabolite names

    • .modelID - (optional) model identifier, used as the default experiment name

    • .description - (optional) model description, used as the default experiment description

  • metData – m x nSamples matrix of metabolite data to write, where m equals size(model.S, 1)

OPTIONAL INPUTS:

  • metSampleNames – Cell array (or single string) of sample names, one per column of metData (default: exp1, exp2, …)

  • fileName – Path of the newt experiment data file to write (default: newtExpData.txt in the current folder)

  • param – Structure with fields:

    • .version - version string written to the file header (default: current timestamp)

    • .name - experiment name (default: model.modelID if present, otherwise aModel)

    • .description - experiment description (default: model.description if present, otherwise aDescription)

    • .color - structure with fields .minValue, .minColor, .zeroValue, .zeroColor, .maxValue, .maxColor defining the color scale (default: red-to-blue scale)

Example

% excerpt of the tab-delimited experiment data file format written by % this function version 1.0 name sample experiment data description Adenoid Cystic Carcinoma 2014 vs 2019 color 0 #FFFFFF 100 #FF0000 gene 2014 2019 RB1 36 12 TP53 36 72 CDKN2A 0 14 MDM2 0 5 CCNE 0 7