prepare_regulon_df: prepare_regulon_df

In saezlab/ocean: metabolic enzyme enrichment analysis

prepare_regulon_df

Description

extract and cleanup the regulon collection correpsonding to the desired penalty

Usage

prepare_regulon_df(
  reaction_set_list_merged,
  penalty,
  filter_imbalance = c(0, 1)
)

Arguments

reaction_set_list_merged	a metabolic-enzyme set collections, as returned by the condense_metabolite_set function
penalty	numeric, the index of the reaction_set_list_merged corresponding to the desired penalty
filter_imbalance	a vector of two numbers, representing the lower and upper bounds to filter imbalanced reaction trees. for example c(0.33,0.67) will filter out any reaction were the upstream branch is longer than 2 time the length of the downstream branch, and vice versa

Value

a regulon dataframe with three columns correposning to the enzme, the target metabolite and the weight

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