dominant: Find the latest-occurring mutation shared by at least a...
In robjohnnoble/demonanalysis: Analysis and plotting of demon data

Description Usage Arguments Value Examples

Find the latest-occurring mutation shared by at least a threshold proportion of cells at a specified time

1	dominant(anc, pop_df, threshold, generation = NA)

`anc`	Dataframe of ancestries, as generated by "ancestry" function
`pop_df`	Dataframe with column names including "Identity" and "Population"
`threshold`	Number between 0 and 1; a genotype must exceed this frequency to be considered dominant
`generation`	Generation at which to make the measurement (default NA corresponds to the final Generation)

Identity of the dominant genotype.

library(ggmuller)
library(dplyr)
phylo <- filter(driver_phylo, CellsPerSample == -1)
pop_df <- get_population_df(phylo)
edges <- get_edges(phylo)
anc <- ancestry(edges)
dominant(anc, pop_df, 0.01)
gens_list <- unique(pop_df$Generation)
dominant(anc, pop_df, 0.01, gens_list[round(length(gens_list) / 2)])