Preprocessing¶
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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
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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
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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
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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