SimulateKinetics: Simulate the kinetics of old and new RNA for given...

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

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")
)

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

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

grandR documentation built on April 4, 2025, 2:27 a.m.