sim_contLabelling: Simulate the continuous labelling model using the gillespie...

In MorrisseyLab/CryptDriftR: Analyse crypt lineage tracing data

Description

The model can be found in the paper "Continuous clonal labeling reveals small numbers of functional stem cells in intestinal crypts and adenomas." Kozar, Morrissey et. al. 2013 Cell Stem Cell

Usage

sim_contLabelling(mu, lambda, Ns, time_points, numSim, Pr = 0.5, raw_sims = F)

Arguments

mu	Stem cell mutation probability.
lambda	Stem cell replacement rate.
Ns	Number of functional stem cells per crypt.
time_points	vector of time point values.
numSim	Number of simulations to run.
Pr	Bias in stem cell replacement Pr = 0.5 is neutral.
raw_sims	If true returns raw simulation output. Otherwise just full and partial crypts (see description).

Value

If the raw_sims option was set to false (default), a matrix with two rows is returned the first being partial crypt frequency and the second monoclonal frequency. If raw_sims is set to true the matrix will have N + 1 rows, where the first row is the number of sims with no labelled crypts, the second 1 label crypt and so on.

Examples

time_points = 100:200
x = sim_contLabelling(mu = 1.1e-4, lambda = 0.1, Ns = 5, time_points = 101:201, numSim = 1e7)

MorrisseyLab/CryptDriftR documentation built on Aug. 7, 2021, 8:22 p.m.