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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.

Usage

SimulateKinetics(
  s = 100 * d,
  d = log(2)/hl,
  hl = 2,
  f0 = NULL,
  min.time = -1,
  max.time = 10,
  N = 1000,
  name = NULL,
  out = c("Old", "New", "Total", "NTR")
)

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

Value

a data frame containing the simulated values

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