target_set_from_forest_2: target_set_from_forest_2

In saezlab/ocean: metabolic enzyme enrichment analysis

target_set_from_forest_2

Description

this function converts a 'forest' representation of a metabolic network into a metabolic-enzyme set

Usage

target_set_from_forest_2(forest, measured_species, penalty = 0.5, verbose = T)

Arguments

forest	a forest representation of a metabolic network. can be used with the tree_without_cofactor
measured_species	character vector, the names of the metabolites that are measured. Must be coherents with identifers in forest
penalty	numeric, the penalty, between 0.1 and 0.9 (0 and 1 work as well but are special cases and shouldn't be used)
verbose	boolean, to display progress

Value

a reaction network in the form of a three column dataframe with enzme, metabolite targets and weights.

saezlab/ocean documentation built on Nov. 12, 2024, 5 a.m.