# Simulate the kinetics of old and new RNA for given parameters.

Source:`R/modeling.R`

`SimulateKinetics.Rd`

The standard mass action kinetics model of gene expression arises from the differential equation \(df/dt = s - d f(t)\), with s being the constant synthesis rate, d the constant degradation rate and \(f0=f(0)\) (the abundance at time 0). The RNA half-life is directly related to d via \(HL=log(2)/d\). This model dictates the time evolution of old and new RNA abundance after metabolic labeling starting at time t=0. This function simulates data according to this model.

## Arguments

- s
the synthesis rate (see details)

- d
the degradation rate (see details)

- hl
the RNA half-life

- f0
the abundance at time t=0

- min.time
the start time to simulate

- max.time
the end time to simulate

- N
how many time points from min.time to max.time to simuate

- name
add a Name column to the resulting data frame

- out
which values to put into the data frame

## Details

Both rates can be either (i) a single number (constant rate), (ii) a data frame with names "offset", "factor" and "exponent" (for linear functions, see ComputeNonConstantParam) or (iii) a unary function time->rate. Functions

## See also

PlotSimulation for plotting the simulation

## Examples

```
head(SimulateKinetics(hl=2)) # simulate steady state kinetics for an RNA with half-life 2h
#> Time Value Type
#> 1 -1.0000000 100 Old
#> 2 -0.9889890 100 Old
#> 3 -0.9779780 100 Old
#> 4 -0.9669670 100 Old
#> 5 -0.9559560 100 Old
#> 6 -0.9449449 100 Old
```