R/format_mutation.R

In jdavilal/excerno: Fillter out somatic mutations generated by the Formalin-Fixed Paraffin-Embedded (FFPE) tissue preservation technique from cancer tissue

#' Format mutation
#'
#' Determine the string format of a position in a genomic sequence
#'
#' @param position The position of the mutation.
#' @param sequence The genomic sequence of type DNAString.
#' @param alternate The alternate base of type character. If left empty, format_mutation() will output only the nucleotide base with its surrounding bases.
#' @return A string of the mutation in a certain format
#' @examples
#'
#' library(Biostrings)
#' library(BSgenome.Hsapiens.UCSC.hg38)
#'  library(stringr)
#'
#' # Load in the sequence
#' seq <- getSeq(Hsapiens, "chr1")
#' format_mutation(20124, seq, "A")
#' @export
format_mutation <- function(position, sequence, alternate = "") {

  # Argument validation
  if (!is.double(position)) { stop("argument position is not of type double") }
  if (class(sequence) != "DNAString") { stop("argument sequence is not of type DNAString") }
  if (!is.character(alternate)) { stop("argument alternate is not of type character") }
  if (str_length(alternate) > 1) { stop("argument alternate must have only one character or none at all") }

  alternate <- toupper(alternate)
  if (!(alternate == "A" || alternate == "T" || alternate == "C" || alternate == "G")) { stop("argument alternate must be A, T, C, or G only") }

  # Returns value base on argument alternate
  if (str_length(alternate) == 1) {
    mutation <- paste(toString(sequence[position - 1]), "[", toString(sequence[position]), ">", alternate, "]", toString(sequence[position + 1]), sep = "")
  } else {
    mutation <- paste(toString(sequence[position - 1]), toString(sequence[position]), toString(sequence[position + 1]), sep = "")
  }

  return (mutation)
}