SimulateKinetics {grandR}

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

Description

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

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

Value

a data frame containing the simulated values

See Also

PlotSimulation for plotting the simulation

Examples

head(SimulateKinetics(hl=2))   # simulate steady state kinetics for an RNA with half-life 2h