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。

1 for (value in dt$value){ 2 #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 -1 3     low=1 4     high=nrow(df) 5     mid=high %/% 2 6     if (df[low,1] <= value & value <= df[low,2]) low 7     else if (df[high,1] <= value & value <= df[high,2]) high 8     else{ 9     while (value > df[mid,2] || value < df[mid,1]){10       if (value > df[mid,2]){11         low = mid+112       } else if (value < df[mid,1]) {13         high = mid - 114       } 15       if(high

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。

1 #!/bin/Rscript 2  3 library(data.table) 4  5 arg <- commandArgs(T) 6 if (length(arg) != 3) { 7     message("[usage]: BedAnnoGene.R bedfile gtffile outputfile") 8     message("    bedfile format: chr start end information(Arbitrary but can not be lacked)") 9     message("    GTFfile: gtf file downloaded from GENCODE")10     message("    outputfile: file to be writen out")11     message("    needed package: data.table 1.10.4")12     stop("Please check your arguments!")13 }14     15 bedfile <- arg[1]16 annofile <- arg[2]17 outfile <- arg[3]18 19 #read file 20 anno <- fread(annofile,sep="\t",header=F)21 bed <- fread(bedfile,sep="\t",header=F)22 setnames(anno,c("V1","V2","V3","V4","V5","V9"),c("Chr","Gene","Type","Start","End","Info"))23 anno <- anno[Type=="gene",.(Chr,Start,End,Gene=sapply(strsplit(tstrsplit(Info,";")[3][[1]],"\""),function(x)x[2]))]24 setkey(anno,Chr,Start,End)25 setkey(bed,V1,V2,V3)26 27 #find overlaps by Chr28 lst <- list()29 for (ChrI in intersect(unique(bed$V1),unique(anno$Chr))){30   anno_reg <- anno[Chr == ChrI,.(Start,End)]31   bed_reg <- bed[V1 == ChrI,.(V2,V3)]32   setkey(anno_reg,Start,End)33   setkey(bed_reg,V2,V3)34   overl <- foverlaps(bed_reg,anno_reg,which=TRUE,nomatch = 0)35   if (nrow(overl) > 0){36     lst[[ChrI]] <- data.table(Chr=ChrI,bed[V1 == ChrI,][overl[["xid"]],.(V2,V3,V4)],anno[Chr == ChrI][overl[["yid"]],.(Gene)])37   }38 }39 merge_dt <- rbindlist(lst)40 setnames(merge_dt,c("V2","V3","V4"),c("Start","End","Name"))41 42 #if one region has more than one gene43 torm <- list()44 for (i in 1:(nrow(merge_dt)-1)){
   if(merge_dt[i,"Name"]==merge_dt[i+1,"Name"]){
   set(merge_dt,i+1L,ncol(merge_dt),paste(merge_dt[i,"Gene"],merge_dt[i+1,"Gene"],sep=";"));torm <- c(torm,list(i))}}45 torm <- unlist(torm)46 merge_dt <- merge_dt[-torm,]47 48 fwrite(merge_dt,file=outfile)

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