R语言实现对基因组SNV进行注释

很多时候，我们需要对取出的SNV进行注释，这个时候可能会在R上进行注释，通常注释文件都含有Chr(染色体)、Start(开始位点)、End(结束位点)、Description（描述），而我们的SNV文件通常是拥有Position（位置），因此我们可以先定位Chr，再用Postion去定位到Start和End之间，找到相对应的Description。为了加快速度，可以使用二分查找法。

 for (value in dt$value){
 #df:data.frame, V1 and V2 should be Start and End   value: Postition  used to find region  return:df row number where position locates  ,if no region return -
     low=
     high=nrow(df)
     mid=high %/%
     if (df[low,] <= value & value <= df[low,]) low
     else if (df[high,] <= value & value <= df[high,]) high
     else{
     while (value > df[mid,] || value < df[mid,]){
       if (value > df[mid,]){
         low = mid+
       } else if (value < df[mid,]) {
         high = mid -
       }
       if(high<low){
          mid=-;break
       }
       mid=(low+high)%/%
     }
       mid
 }
 }

在R中使用for循环效率低，因此也可以用data.table包的foverlap函数，改进代码如下，对bed文件进行注释，如果要对snv进行注释，只需要将snv改成相应的start和end相等的bed文件即可。

 #!/bin/Rscript

 library(data.table)

 arg <- commandArgs(T)
 if (length(arg) != ) {
     message("[usage]: BedAnnoGene.R bedfile gtffile outputfile")
     message("    bedfile format: chr start end information(Arbitrary but can not be lacked)")
     message("    GTFfile: gtf file downloaded from GENCODE")
     message("    outputfile: file to be writen out")
     message("    needed package: data.table 1.10.4")
     stop("Please check your arguments!")
 }

 bedfile <- arg[]
 annofile <- arg[]
 outfile <- arg[]

 #read file
 anno <- fread(annofile,sep="\t",header=F)
 bed <- fread(bedfile,sep="\t",header=F)
 setnames(anno,c("V1","V2","V3","V4","V5","V9"),c("Chr","Gene","Type","Start","End","Info"))
 anno <- anno[Type=="gene",.(Chr,Start,End,Gene=sapply(strsplit(tstrsplit(Info,";")[][[]],"\""),function(x)x[]))]
 setkey(anno,Chr,Start,End)
 setkey(bed,V1,V2,V3)

 #find overlaps by Chr
 lst <- list()
 for (ChrI in intersect(unique(bed$V1),unique(anno$Chr))){
   anno_reg <- anno[Chr == ChrI,.(Start,End)]
   bed_reg <- bed[V1 == ChrI,.(V2,V3)]
   setkey(anno_reg,Start,End)
   setkey(bed_reg,V2,V3)
   overl <- foverlaps(bed_reg,anno_reg,which=TRUE,nomatch = )
   if (nrow(overl) > ){
     lst[[ChrI]] <- data.table(Chr=ChrI,bed[V1 == ChrI,][overl[["xid"]],.(V2,V3,V4)],anno[Chr == ChrI][overl[["yid"]],.(Gene)])
   }
 }
 merge_dt <- rbindlist(lst)
 setnames(merge_dt,c("V2","V3","V4"),c("Start","End","Name"))

 #if one region has more than one gene
 torm <- list()
 for (i in :(nrow(merge_dt)-)){if(merge_dt[i,"Name"]==merge_dt[i+,"Name"]){set(merge_dt,i+1L,ncol(merge_dt),paste(merge_dt[i,"Gene"],merge_dt[i+,"Gene"],sep=";"));torm <- c(torm,list(i))}}
 torm <- unlist(torm)
 merge_dt <- merge_dt[-torm,]

 fwrite(merge_dt,file=outfile)

使用帮助可以在我github看到   https://github.com/yiliu4234/BedAnnoGene