Just now there are three genes (driver, neutral and deletereous). However, this is clearly not enough as the number of driver sites are a quite large proportion of the sites, so the evolution of these sites are to quick. In order to avoid this and try to be a bit more realistic we need to simulate different number of "genes" for the different types. For example 1 driver gene, 100 neutrals and 10 deletereous, all with the same size. In order to do this extensible for different numbers it should be added as a parameter in the run_simulation2.R script. extract_results. R shouls be also changed to handle the different number of genes and generate reasonable amount of outputs.

Ideally from a single cell, although for this maybe it could harbor a driver mutation (to avoid "sudden death")

Like parameters as number of sites and number of genes and proportion of effect. This would facilitate the downstream analyses.

Currently if a oncoSimulR replicate fails (doesn't reach cancer) the run_simulation2.R script stops.

In the output