Transcriptomics¶
-
createTissueSpecificModel
(model, options, funcModel, exRxnRemove, optionalParams)[source]¶ Creates draft tissue specific model from mRNA expression data
Usage
tissueModel = createTissueSpecificModel(model, options)Input
- model – model strusture
- options: structure field containing method specific
- informations
- .solver: Use either ‘GIMME’,’iMAT’,’INIT’,’MBA’,
- ‘mCADRE’,’fastCore’
.additionalparam: see NOTE section below
Optional inputs
- funcModel – 1 - Build a functional model having only reactions that can carry a flux (using a consistency check), 0 - skip this step (Default = 0)
- exRxnRemove – Names of exchange reactions to remove (Default = [])
- optionalParams Additional paramaters for the consistency
- check. Will only be used if funcModel = 1 Is a structure with possible fields of epsilon (numeric, min nonzero mass), modeFlag (return flux mode, 0/1), and method (‘fastcc’,’dc’)
Output
- tissueModel – extracted model
NOTES: This section describes the additional parameter fields that need to be set in ‘options’ structure depending on the solver used. Some of these are optional (marked by an ‘*’), if not defined, they will be set at their default values.
- for iMAT
- options.expressionRxns reaction expression, expression data corresponding to model.rxns.
- Note : If no gene-expression data are available for the reactions, set the value to -1
- options.threshold_lb lower bound of expression threshold, reactions with
- expression below this value are “non-expressed”
- options.threshold_ub upper bound of expression threshold, reactions with
- expression above this value are “expressed”
- options.tol* minimum flux threshold for “expressed” reactions
- (default 1e-8)
- options.core* cell with reaction names (strings) that are manually put in
- the high confidence set (default - no core reactions)
options.logfile* name of the file to save the MILP log (defaut - ‘MILPlog’) options.runtime* maximum solve time for the MILP (default - 7200s) options.epsilon* small value to consider when modeling
flux (default 1)
- for GIMME
- options.expressionRxns reaction expression, expression data corresponding to model.rxns.
- Note : If no gene-expression data are available for the reactions, set the value to -1
options.threshold expression threshold, reactions below this are minimized options.obj_frac* minimum fraction of the model objective function
(default - 0.9)- for INIT
- options.weights column with positive (high expression) and negative
- (low expression) weights for each reaction
- options.tol* minimum flux threshold for “expressed” reactions
- (default - 1e-8)
options.logfile* name of the file to save the MILP log (defaut - ‘MILPlog’)
options.runtime* maximum solve time for the MILP (default - 7200s) options.epsilon* small value to consider when modeling
flux (default 1)- for MBA
options.medium_set list of reaction names with medium confidence options.high_set list of reaction names with high confidence options.tol* minimum flux threshold for “expressed” reactions
(default - 1e-8)- for mCADRE
- options.ubiquityScore ubiquity scores, vector of the size of ‘model.rxns’
- quantifying how often a gene is expressed accross samples.
- options.confidenceScores literature-based evidence for generic model,
- vector of the size of ‘model.rxns’
- options.protectedRxns* cell array with reactions names that are manually added to
- the core reaction set (default- no reactions)
- options.checkFunctionality* Boolean variable that determine if the model should be able
- to produce the metabolites associated with the protectedRxns
- 0: don’t use functionality check (default value) 1: include functionality check
- options.eta* tradeoff between removing core and zero-expression
- reactions (default - 1/3)
- options.tol* minimum flux threshold for “expressed” reactions
- (default - 1e-8)
- for fastCore
- options.core indices of reactions in cobra model that are part of the
- core set of reactions
- options.epsilon* smallest flux value that is considered
- nonzero (default 1e-4)
options.printLevel* 0 = silent, 1 = summary, 2 = debug (default 0)