Description Usage Arguments Value Examples
View source: R/stochastic_simulation.R
Simulates (stochastically) the behaviour of an in silico system over time using parallelisation, i.e. the expression of the different genes.
1 2 3 4 5 6 7 8 9 10 11 12 13 | simulateParallelInSilicoSystem(
insilicosystem,
insilicopopulation,
simtime,
nepochs = -1,
ntrials = 1,
simalgorithm = "Direct",
writefile = F,
filepath = NULL,
filename = "simulation",
no_cores = parallel::detectCores() - 1,
ev = getJuliaEvaluator()
)
|
insilicosystem |
The in silico system to be simulated (see
|
insilicopopulation |
The in silico population to be simulated (see
|
simtime |
The final time of the simulation (in seconds). |
nepochs |
The number of times to record the state of the system during the simulation. |
ntrials |
The number of times the simulation must be replicated (for each individual). |
simalgorithm |
The name of the simulation algorithm to use in the Julia
function |
writefile |
Does the julia function write the species and reactions lists in a text file? |
filepath |
If writefile = |
filename |
If writefile = |
no_cores |
The number of cores to use for the simulation. By default use
the function |
ev |
A Julia evaluator. If none provided select the current evaluator or create one if no evaluator exists. |
A list composed of:
Simulation
: A data-frame
with the simulated expression profiles of the genes for the different
individuals in the in silico population. For gene i, "Ri" corresponds to
the RNA form of the gene, "Pi" to the protein form of the gene. The suffix
"GCNj" indicates that the molecule comes from the j-th allele of the gene.
runningtime
: The running time (elapsed seconds) of the
parallel simulation (only 1 value).
stochmodel
: A Julia proxy
object to retrieve the stochastic system in the Julia evaluator.
1 2 3 4 5 6 | mysystem = createInSilicoSystem(G = 5, regcomplexes = "none", ploidy = 2)
mypop = createInSilicoPopulation(15, mysystem)
sim = simulateParallelInSilicoSystem(mysystem, mypop, 1000)
head(sim$Simulation)
## Visualising the result
plotSimulation(sim$Simulation)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.