`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()

model | A dyngen intermediary model for which the feature network has been generated with |
---|

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() # }