coregflux_static {CoRegFlux} | R Documentation |
coregflux_static()
uses the gene states to update the fluxes bounds
from the metabolic model.
coregflux_static(model, predicted_gene_expression, gene_parameter = 0, tol = 1e-10, aliases = NULL)
model |
A genome-scale metabolic model of class modelorg |
predicted_gene_expression |
The vector of predicted gene expression for
the genes present in the metabolic model as given by
|
gene_parameter |
Parameter of the softplus function |
tol |
Fluxes values below this threshold will be ignored. |
aliases |
a data.frame containing the gene names currently used in the network under the colname "geneName" and the alias under the colnames "alias" |
list containing:
model |
the metabolic model with the coregflux constraints added |
softplus_positive |
the results of evaluating ln(1+exp(gpr(x+theta))) where gpr() are the continuous version of the gpr rules applied to a set of gene expression x |
softplus_negative |
the results of evaluating ln(1+exp(gpr(x+theta))) where gpr() are the continuous version of the gpr rules applied to a set of gene expression x |
data("SC_GRN_1") data("SC_experiment_influence") data("SC_EXP_DATA") data("aliases_SC") data(iMM904) data(PredictedGeneState) static_list<-coregflux_static(iMM904,PredictedGeneState)