Math_modeling/README.md

In SunPathLab/Butte: BoUnds of Time Till Expansion, inferring the SCNA arrival time in the somatic evolution toward the most recent common ancestor of tumor sample(s).

Model Description:

The tumor starts with a single tumor-initiating cell. \ The tumor-initiating cell and its descendants with only passenger mutations form the Type 0 population. \ Type 0 cells give birth at a rate of a_0 and die at a rate of b_0. \ Type 0 cells mutate to Type 1 cells at a rate of u_1. \ Type 1 cells give birth at a rate of a_1 and die at a rate of b_1. \ Both Type 0 and Type 1 cells accumulate passenger mutations at a rate of u_0. \ This package simulates the number of passenger mutations shared by more than a certain percentage (denoted by a threshold) of descendents of the first Type 1 cell when the size of its living descendents reaches 10,000.

Run (in Matlab environment):

#1. assign values to parameters. A code example is as follows:
    a_0=1;
    b_0=1;
    a_1=2;
    b_1=1;
    u_0=0.1;
    u_1=0.0001;
    threshold=0.9;

#2. run
[time_to_first_type_1_cell, num_of_passenger_mutation]=main(a_0,b_0,a_1,b_1,u_0,u_1,threshold)

output: \ time_to_first_type_1_cell: the birth time of the first type 1 cell with at least 10,000 living descendents at some time point.\ num_of_passenger_mutation: the number of passenger mutations shared by more than [threshold] of descendents of the first type 1 cell when the size of its living descendents reaches 10,000.

SunPathLab/Butte documentation built on Sept. 19, 2023, 9:42 a.m.