R/mut_type.R

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

#' Retrieve base substitution types from a VCF object
#'
#' A function to extract the base substitutions from a vcf and translate to
#' the 6 common base substitution types.
#'
#' @param vcf A CollapsedVCF object
#' @return Character vector with base substitution types
#'
#' @examples
#' ## See the 'read_vcfs_as_granges()' example for how we obtained the
#' ## following data:
#' vcfs <- readRDS(system.file("states/read_vcfs_as_granges_output.rds",
#'   package = "MutationalPatterns"
#' ))
#'
#' mut_type(vcfs[[1]])
#' @seealso
#' \code{\link{read_vcfs_as_granges}}
#'
#' @export

mut_type <- function(vcf) {
  muts <- mutations_from_vcf(vcf)
  types <- unlist(muts)
  types <- gsub("G>T", "C>A", types)
  types <- gsub("G>C", "C>G", types)
  types <- gsub("G>A", "C>T", types)
  types <- gsub("A>T", "T>A", types)
  types <- gsub("A>G", "T>C", types)
  types <- gsub("A>C", "T>G", types)
  return(types)
}