create_reaction_adjacency_matrix: Create adjacency matrix from reactions

In michaelwitting/wormLipidPredictR: Lipid reaction prediction based on WormJam

Create adjacency matrix from reactions

Description

The function create_reaction_adjacency_matrix creates an adjacency matrix connecting substrates and products that are linked by reactions.

Usage

create_reaction_adjacency_matrix(reaction_l)

Arguments

reaction_l

list as obtained from create_reactions

Details

The function create_reaction_adjacency_matrix accepts the output of the create_reactions function.

The adjacency matrix can be used in subsequent analysis for network analysis, e.g. by converting the adjacency matrix to a graph via igraph::graph_from_adjacency_matrix.

Value

matrix

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),
    c(4, "RHEA:27429", "M_H2O + M_PA = M_Pi + M_1,2-DG", 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)

## create the adjacency matrix
create_reaction_adjacency_matrix(reaction_l)

michaelwitting/wormLipidPredictR documentation built on Nov. 24, 2024, 5:39 p.m.