查找相邻基因突变

这是一个从22万多个基因突变里，挑选相邻100bp以内的基因突变对的代码

for(chromos in unique(maflength$Chromosome)){

  for(samps in unique(maflength$Tumor_Sample_Barcode)){

    maf <- maflength[maflength$Chromosome == chromos&

                      maflength$Tumor_Sample_Barcode == samps, ]

    if(nrow(maf) >= 2){

      for(i in 1:(nrow(maf)-1)){

        j = i +1

        while(j <= nrow(maf)){

          if(all(!is.na(maf$Start_Position[j]), !is.na(maf$Start_Position[i]))&abs(maf$Start_Position[j] - maf$Start_Position[i]) <= 100){

            GenDist <- data.frame(Mut1 = maf$Hugo_Symbol[i],

                                  Mut1StarPos = maf$Start_Position[i],

                                  Mut1EndPos = maf$End_Position[i],

                                  Mut2 = maf$Hugo_Symbol[j],

                                  Mut2StarPos = maf$Start_Position[j],

                                  Mut2EndPos = maf$End_Position[j],

                                  Chromosome = chromos,

                                  SampleBarCode = samps)

            Gens <- rbind(Gens, GenDist)

            j <- j + 1

          }

          else break

        }

      }

    }

    else break

  }

}