GRB_generate_set_lists_cluster: Function for PACT method

In DikshantPradhan/FluxCouplingTools:

Description

Function for PACT method

Usage

GRB_generate_set_lists_cluster(model_og, suppression_idxs = -1,
  reaction_indexes = c(), compare_known_init_sets = FALSE,
  optimize_suppr = FALSE, optimize_rxns = FALSE, cores = 1,
  avoid_idxs = c(), file_output = NULL)

Arguments

model_og	model upon which to run PACT
suppression_idxs	list of integers indicating indexes of reactions to iteratively block and calculate coupling for. DEFAULT is -1, which indicates that all reactions should be suppressed
reaction_indexes	list of integers indicating indexes of reaction to check coupling for. DEFAULT is empty list, which indicates that all reactions in the model should be considered
compare_known_init_sets	boolean indicating whether or not to calculate R0 sets in order to run further optimizations during flux coupling and PACT. DEFAULT: FALSE
optimize_suppr	boolean indicating whether or not to optimize the reactions to suppress based on R0 sets. DEFAULT: FALSE
optimize_rxns	boolean indicating whether or not to optimize the reactions couple. DEFAULT: FALSE
cores	integer indicating the number of cores to run on, if intending to parallelize
avoid_idxs	list of integers indicating indexes to specifically avoid suppressing during PACT method
file_output	filename to output coupling vector to

Value

a coupling list: list of list of integers which each indicate the couplings induced by each suppression. The index position of each list indicates the index of the reaction which was suppressed and the integers in eacch list indicate the positions of TRUE values in the coupling array

DikshantPradhan/FluxCouplingTools documentation built on Aug. 27, 2019, 2:19 a.m.