Preprocessing

GPRparser(model, getCNFSets)[source]

Maps the GPR rules of the model to a specified format that is used by the model extraction methods

Usage

parsedGPR = GPRparser(model)

Input

  • model – cobra model structure

Optional input

  • getCNFSets – whether to get the CNF sets (true) or DNF sets (false). DNF sets represent functional enzyme complexes, while CNF sets represent the possible subunits of a complex. (default: false , i.e. DNF sets)

Output

  • parsedGPR – cell matrix containing parsed GPR rule

AUTHORS: Thomas Pfau & Anne Richelle, May 2017

findUsedGenesLevels(model, exprData, printLevel)[source]

Returns vectors of gene identifiers and corresponding gene expression levels for each gene present in the model (‘model.genes’).

Usage

[gene_id, gene_expr] = findUsedGenesLevels(model, exprData)

Inputs

  • model – input model (COBRA model structure)

  • exprData – mRNA expression data structure .gene cell array containing GeneIDs in the same

    format as model.genes

    .value Vector containing corresponding expression value (FPKM)

Optional input

  • printLevel – Printlevel for output (default 0);

Outputs

  • gene_id – vector of gene identifiers present in the model that are associated with expression data
  • gene_expr – vector of expression values associated to each ‘gened_id’

Authors: - S. Opdam & A. Richelle May 2017

mapExpressionToReactions(model, expressionData, minSum)[source]

Determines the expression data associated to each reaction present in the model

Usage

[expressionRxns parsedGPR] = mapExpressionToReactions(model, expressionData)

Inputs

  • model model strusture
  • expressionData mRNA expression data structure
.gene cell array containing GeneIDs in the same
format as model.genes
.value Vector containing corresponding expression
value (FPKM/RPKM)

Optional input

  • minSum – instead of using min and max, use min for AND and Sum for OR (default: false, i.e. use min)

Outputs

  • expressionRxns – reaction expression, corresponding to model.rxns.
  • parsedGPR – cell matrix containing parsed GPR rule
selectGeneFromGPR(model, gene_names, gene_exp, parsedGPR, minSum)[source]

Map gene expression to reaction expression using the GPR rules. An AND will be replaced by MIN and an OR will be replaced by MAX.

Usage

expressionCol = selectGeneFromGPR(model, gene_names, gene_exp, parsedGPR, minMax)

Inputs

  • model – COBRA model struct
  • gene_names – gene identifiers corresponding to gene_exp. Names must be in the same format as model.genes (column vector) (as returned by “findUsedGeneLevels.m”)
  • gene_exp – gene FPKM/expression values, corresponding to names (column vector) (as returned by “findUsedGeneLevels.m”)
  • parsedGPR – GPR matrix as returned by “GPRparser.m”

Optional input

  • minSum – instead of using min and max, use min for AND and Sum for OR

Output

  • expressionCol – reaction expression, corresponding to model.rxns. No gene-expression data and orphan reactions will be given a value of -1.

AUTHOR: Anne Richelle, May 2017