obtain_ChEBI_of_feature: Obtain ChEBI ids of features

In michaelwitting/wormLipidPredictR: Lipid reaction prediction based on WormJam

Obtain ChEBI ids of features

Description

Lipid species are attributed to classes. These classes can be identified via the ChEBI ids in reactions_l. The function obtains the corresponding ChEBI ids for the features and returns a data.frame that contains the mappings between lipid species and lipid classes.

Mappings between the metabolites and ChEBI ids will be done via the data structure of reaction_l, as returned by create_reactions.

Usage

obtain_ChEBI_of_feature(reaction_l)

Arguments

reaction_l

list as obtained from create_reactions

Details

The function obtain_ChEBI_of_feature accepts the output of the create_reactions function. From create_reactions, the ChEBI ids will be inferred.

Value

data.frame

Author(s)

Thomas Naake, [e-mail]

Examples

FA <- c("FA(12:0)", "FA(14:0)", "FA(16:0)")

## create data.frame with reactions and reaction order
reactions <- rbind(
    c(1, "RHEA:15421", "M_ATP + M_CoA + M_FA = M_PPi + M_AMP + M_AcylCoA", FALSE),
    c(2, "RHEA:15325", "M_Glycerol-3-P + M_AcylCoA = M_CoA + M_LPA", FALSE),
    c(3, "RHEA:19709", "M_AcylCoA + M_LPA = M_CoA + M_PA", FALSE)
)
reactions <- data.frame(order = reactions[, 1], reaction_RHEA = reactions[, 2],
    reaction_formula = reactions[, 3], directed = reactions[, 4])
reactions$order <- as.numeric(reactions$order)
reactions$directed <- as.logical(reactions$directed)

## create the list with reactions
reaction_l <- create_reactions(substrates = list(FA = FA), reactions = reactions)

## run the function
obtain_ChEBI_of_feature(reaction_l = reaction_l)

michaelwitting/wormLipidPredictR documentation built on Jan. 30, 2025, 12:30 a.m.