MutationalSignatures_Fittingtool/votes_to_sieve.R at master · MathieuRita/MutationalSignatures_Fittingtool · GitHub

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remove_specific_signatures=function(samples,signatures,set_of_signature,cutoff=0.01){

  #BASELINE SCORE
  boot_1=fit_to_signatures(samples,as.matrix(signatures[,set_of_signature]))
  baseline=RSS(rowMeans(samples),rowMeans(boot_1$reconstructed))

  new_best_score=0

  continue=T
  while(continue){
    #This condition is to prevent from a bug -> fitting with no signature (2 can be replaced by 1)
    continue=F
    if(length(set_of_signature)>2){
      #REMOVE STEPS
      RSSs=c()
      stds=c()
      for(i in seq(1,length(set_of_signature))){
        boot_1=fit_to_signatures(samples,as.matrix(signatures[,set_of_signature[-i]]))
        RSSs=c(RSSs,RSS(rowMeans(samples),rowMeans(boot_1$reconstructed)))
        stds=c(stds,std.error(signatures[,set_of_signature[i]]))
      }

      ind=which.min(RSSs*stds)

      new_best_score=(RSSs[ind]-baseline)/baseline


      if(new_best_score<cutoff){
        set_of_signature=set_of_signature[-ind]
        continue=T
      }
    }
  }

  return(set_of_signature)
}