dot-create_reaction: Create reaction for a given reaction of lipid metabolism

In michaelwitting/wormLipidPredictR: Lipid reaction prediction based on WormJam

Create reaction for a given reaction of lipid metabolism

Description

The function .create_reaction creates from a given template reaction the specific reaction given a set of substrates.

The function returns a list of the products of the reaction (in the first entry of the returned list), together with the template with the updated reactions (in the second entry of the returned list).

Usage

.create_reaction(
  substrates,
  template = NULL,
  reaction = "RHEA:15421",
  constraints = character(length(substrates)),
  negate = logical(length(substrates))
)

Arguments

substrates	list, with entry names equal to substrates
template	data.frame
reaction	character(1)
constraints	character, with length length(substrates)
negate	logical, with length length(substrates)

Details

If template == NULL, the function will load a template specific to the reaction with mininum information on the reaction.

Value

list of length 2

Author(s)

Michael Witting, [e-mail] and Thomas Naake, [e-mail]

Examples

FA <- c("FA(14:0(12Me))", "FA(16:0(14Me))", "FA(15:1(9Z)(14Me))",        
    "FA(17:0(16Me))", "FA(12:0(11Me))", "FA(13:0(12Me))", "FA(14:0(13Me))",
    "FA(15:0(14Me))", "FA(16:0(15Me))", "FA(12:0)", "FA(14:0)")
    
template <- list(reaction_name = "CoA biosynthesis", 
    reaction_formula = "M_ATP + M_CoA + M_FA = M_PPi + M_AMP + M_AcylCoA",
    reaction_RHEA = "RHEA:15421",
    reaction_isReversible = "",
    reaction_geneAssociation = "",
    reaction_pathway = "Acyl-CoA synthetase")
 
## run create_reaction (template = NULL)
.create_reaction(substrates = list(FA = FA), template = NULL,
    reaction = "RHEA:15421")
    
## run create_reaction (template = template)
.create_reaction(substrates = list(FA = FA), template = template,
    reaction = "RHEA:15421")

michaelwitting/wormLipidPredictR documentation built on July 1, 2023, 9:20 p.m.