R/interference.R

In sarahodell/magicsim: What the Package Does (One Line, Title Case)

#' If the two crossover events are too close to each other,
#' only keep one of the crossover locations
#' @param xo_pos crossover position (int)
#' @param dist physical distance below which interference occurs (default is 100 kb)
#' @export


interference <- function(xo_pos,maxp,dist=1e5){
  while(sum(diff(xo_pos) < dist) != 0){
    closest=c(which.min(diff(xo_pos)),which.min(diff(xo_pos))+1)
    choice=sample(closest,1)
    if(xo_pos[choice]+(2*dist) < maxp){
      xo_pos[choice]=xo_pos[choice]+(2*dist)
    }
    else{
      xo_pos[choice]=xo_pos[choice]-(2*dist)
    }

  }
  return(xo_pos)
}