generate_kinetics() samples the kinetics of genes in the feature network for which
the kinetics have not yet been defined.
kinetics_default() is used to configure parameters pertaining this process.
kinetics_random_distributions() will do the same, but the distributions are also
randomised.
generate_kinetics(model)
kinetics_default()
kinetics_random_distributions()A dyngen intermediary model for which the feature network has been generated with generate_feature_network().
A dyngen model.
To write different kinetics settings, you need to write three functions
with interface function(feature_info, feature_network, cache_dir, verbose).
Described below are the default kinetics samplers.
sampler_tfs() mutates the feature_info data frame by adding the following columns:
transcription_rate: the rate at which pre-mRNAs are transcribed,
in pre-mRNA / hour. Default distribution: U(1, 2).
translation_rate: the rate at which mRNAs are translated into proteins,
in protein / mRNA / hour. Default distribution: U(100, 150).
mrna_halflife: the half-life of (pre-)mRNA molecules, in hours.
Default distribution: U(2.5, 5).
protein_halflife: the half-life of proteins, in hours.
Default distribution: U(5, 10).
splicing_rate: the rate at which pre-mRNAs are spliced into mRNAs,
in reactions / hour. Default value: log(2) / (10/60), which corresponds to a half-life of 10 minutes.
independence: the degree to which all regulators need to be bound for transcription to occur (0), or
whether transcription can occur if only one of the regulators is bound (1).
sampler_nontfs() samples the transcription_rate, translation_rate,
mrna_halflife and protein_halflife from a supplementary file of Schwannhäusser et al.,
2011, doi.org/10.1038/nature10098. splicing_rate is by default the same as in sampler_tfs().
independence is sampled from U(0, 1).
sampler_interactions() mutates the feature_network data frame by adding the following columns.
effect: the effect of the interaction; upregulating = +1, downregulating = -1.
By default, sampled from -1, 1 with probabilities .25, .75.
strength: the strength of the interaction. Default distribution: 10^U(0, 2).
hill: the hill coefficient. Default distribution: N(2, 2) with a minimum of 1 and a maximum of 10.
dyngen on how to run a complete dyngen simulation
model <-
initialise_model(
backbone = backbone_bifurcating(),
kinetics_params = kinetics_default()
)
# \donttest{
data("example_model")
model <- example_model %>%
generate_kinetics()
# }