SimulateKinetics: 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,
dropout = 0,
min.time = -1,
max.time = 10,
N = 1000,
name = NULL,
out = c("Old", "New", "Total", "NTR")
)
Value
a data frame containing the simulated values
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
dropout
the 4sU dropout factor
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