R/mutator_uniform.R

In philliplab/yasss: Yet Another Short Sequence Simulator

#' The uniform mutator
#'
#' Mutates a sequence giving each base an equal chance to experience a random mutation
#'
#' @param parent A character string containing the DNA sequence of the parent
#' @param mu A single number between 0 and 1 specifying the per base mutation rate
#' @export

mutator_uniform_fun <- function(parent, mu){

  if (length(parent) != 1){
    stop("The length of the parent argument to a mutator must be 1")
  }

  parent <- strsplit(as.character(parent), '')[[1]]

  mut_spots <- which(runif(length(parent)) < mu)
  child <- parent

  if (length(mut_spots > 0)){
    for (mut_spot in mut_spots){
      child[mut_spot] <- sample(setdiff(c('A', 'C', 'G', 'T'), child[mut_spot]), 1)
    }
  }

  parent <- paste(parent, sep = '', collapse = '')
  child <- paste(child, sep = '', collapse = '')

  result <- list(parent = parent,
                 child = child,
                 mutation_stats = list(n_mut = length(mut_spots)),
                 mu = mu)
  return(result)
}