View source: R/create_reaction.R
create_reaction_adjacency_matrix creates an adjacency
matrix connecting substrates and products that are linked by reactions.
list as obtained from
create_reaction_adjacency_matrix accepts the output of
The adjacency matrix can be used in subsequent analysis for network analysis,
e.g. by converting the adjacency matrix to a graph via
Thomas Naake, email@example.com
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], RHEA = reactions[, 2], reactions = 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)
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