R/detect_kataegis.R

In maftools: Summarize, Analyze and Visualize MAF Files

# Kategis detection algorithm by Moritz Goretzky @ WWU Munster, which exploits the definition of Kategis (six consecutive mutations with an avg. distance of 1000bp ) to idetify hyper mutated genomic loci.
# An algorithm which starts with a double-ended queue to which six consecutive mutations are added and their average intermutation distance is calculated.
# If the average intermutation distance is larger than 1000, one element is added at the back of the queue and one is removed from the front.
# If the average intermutation distance is less or equal to 1000, further mutations are added until the average intermutation distance is larger than 1000.
# After that all mutations in the double-ended queue are written into output as one kataegis and the double-ended queue is reinitialized with six mutations.

detect_kataegis_chr = function(chr.dat){
  chr.dat[, row_idx := 1:nrow(chr.dat)]

  start_idx = 1
  end_idx = 6
  queue = chr.dat[start_idx:end_idx]

  kat_loc = data.table::data.table()
  kat_id = 1

  while(end_idx <= nrow(chr.dat)){

    if(mean(diff(queue[, Start_Position], na.rm = TRUE), na.rm = TRUE) > 1000){
      start_idx = start_idx+1
      end_idx = end_idx+1
      queue = chr.dat[start_idx:end_idx]
    }else{

      while( mean(diff(queue[, Start_Position], na.rm = TRUE), na.rm = TRUE) <= 1000 &
             end_idx <= nrow(chr.dat) ){
        end_idx = end_idx+1
        queue = chr.dat[start_idx:end_idx]
      }

      #---Summarize kat loci
      x = chr.dat[(start_idx):c(end_idx-1)]  # start_idx not incremented after kat detected
      ycp = data.table::data.table(Chromosome = unique(as.numeric(as.character(x[,Chromosome]))),
                                   Start_Position = x[,min(Start_Position)],
                                   End_Position = x[,max(Start_Position)],
                                   nMuts = nrow(x),
                                   Avg_intermutation_dist = mean(x[,diff(Start_Position)]))
      ycp[,Size := End_Position - Start_Position]

      ycp = cbind(ycp,
                  data.table::dcast(data = x[,.N,.(con.class, Tumor_Sample_Barcode)],
                                    Tumor_Sample_Barcode ~ con.class, value.var = 'N'))

      kat_loc = data.table::rbindlist(l = list(kat_loc, ycp), fill = TRUE, use.names = TRUE)
      #---

      start_idx = end_idx
      end_idx = end_idx+6
      queue = chr.dat[(start_idx):(end_idx)]
    }
  }
  kat_loc
}


detect_kataegis = function(maf.snp){
  chr.spl = split(maf.snp, maf.snp$Chromosome)
  kloci = lapply(chr.spl, detect_kataegis_chr)
  kloci = data.table::rbindlist(l = kloci, fill = TRUE, use.names = TRUE)
  if(nrow(kloci) > 0){
    #kloci[,Filter := "PASS"]
    message('Kataegis detected at:')
    print(kloci)
    write.table(x = kloci,
                file = paste(unique(kloci[,Tumor_Sample_Barcode]), 'Kataegis.tsv', sep='_'),
                sep='\t', quote = FALSE, row.names = FALSE)
  }
  kloci
}