KEGG¶
- createUniversalReactionModel(KEGGFilename, KEGGBlackList)¶
Creates the U matrix using the universal data from the KEGG database
USAGE:
KEGG = createUniversalReactionModel(KEGGFilename, KEGGBlackList)
- INPUTS:
KEGGFilename: downloaded from KEGG database (ie. ‘reaction.lst’) KEGGBlackList: KEGG reactions not to use
- OUTPUT:
KEGG: U Matrix
- mapKEGGID2Model(model, Dictionary)¶
This function matches the compound abreviation in model and from CompAbr and connects with the model metabolite the corresponding KEGGID
USAGE:
model = mapKEGGID2Model(model, Dictionary)
- INPUTS:
model: COBRA model structure Dictionary: consists of:
CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)
KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr
- OUTPUT:
model: KEGG model structure
- mapMetName2KEGGID(model, Dictionary)¶
This function maps names of metabolites to KEGG IDs.
USAGE:
model = mapMetName2KEGGID(model, Dictionary)
- INPUTS:
model: KEGG model structure Dictionary: consists of:
CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)
KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr
- OUTPUT:
model: COBRA model structure
- transformKEGG2Model(modelKEGG, dictionary)¶
Translates the metabolites from KEGG to cobra model names.
USAGE:
model = mapMetName2KEGGID(model, Dictionary)
- INPUTS:
model: KEGG model structure Dictionary: consists of:
CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)
KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr
- OUTPUT:
model: COBRA model structure
- transformModel2KEGG(model, Dictionary)¶
Replaces model.mets with model.metKEGGID. If no KEGGID defined, the empty cell will be replaced with metabolite abreviation.
USAGE:
modelKEGG = transformModel2KEGG(model, Dictionary)
- INPUTS:
model: COBRA model structure Dictionary: consists of:
CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)
KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr
- OUTPUT:
modelKEGG: KEGG model structure