get_mutation_df: 'get_mutation_df' Converts sizes to the frequency of the...
In MathOnco/EvoFreq: Clonal Dynamic Visualizations

get_mutation_df Converts sizes to the frequency of the mutations in the population

1	get_mutation_df(clone_size_df, clones, parents)

`clone_size_df`	Dataframe in a wide format, where each row corrsponds to a single clone, and the columns are the sizes of that clone at each timepoint
`clones`	Array containing the clone ids. The index of each clone must correspond to the same index of the row in `size_df` that contains the sizes of that clone over time
`parents`	Array containing the ids of the parent of each clone in the `clones` array.

data("example.easy.wide")
### Split dataframe into clone info and size info using fact timepoint column names can be converted to numeric values
time_col_idx <- suppressWarnings(which(! is.na(as.numeric(colnames(example.easy.wide)))))
attribute_col_idx <-suppressWarnings(which(is.na(as.numeric(colnames(example.easy.wide)))))
attribute_df <- example.easy.wide[, attribute_col_idx]
size_df <- example.easy.wide[, time_col_idx]
parents <- example.easy.wide$parents
clones <- example.easy.wide$clones
### Size data can be converted to mutation counts for additional analyses, like calculating mutation frequencies
mutation_count_df <- get_mutation_df(size_df, clones, parents)
total_chromosomes <- 2*colSums(size_df) ### Calculation assumes that mutations are on a single chromosome
allele_frequency_df <- sweep(mutation_count_df,2,total_chromosomes,"/")