cytoband坐标+gencode注释一步get基因名

想去这样的实验室，图源水印

需要下载两个文件：

cytoband文件

gencode注释文件

用到的包：

if(!require(GenomicRanges)){
  BiocManager::install("GenomicRanges")
  library(GenomicRanges)
}

文件下载到本地后，简单粗暴读取

cytobandfile <- read.csv("cytoBand.txt.gz", sep = "\t",header = F)
gencodeinfo <- read.csv("gencode_v29_human_gene_info",sep = "\t",header = F)

先对 cytobandfile 做些文本处理

cytobandfile$band <- gsub("[[:alpha:]]","",cytobandfile$V4)
cytobandfile$arm <- gsub("\\d.+","",cytobandfile$V4)
colnames(cytobandfile) <- c("chr","start","end", "stain","band","arm")
cytobandfile <- cytobandfile[,-4]  ##其实不把 p,q 和数字分开似乎更方便
cytobandfile$gene_name <- NA

gencodeinfo 输入正确列名

colnames(gencodeinfo) <- c("gene_name", "gene_type", "gene_id",
                           "seqnames", "start", "end")

一步get时间到：

Chrloc2Sym <- function(cytobandfile,gencodeinfo,arm,band) {
  ## 构建cytoband GRanges
  cytobandgr <-  GRanges(seqnames = Rle(cytobandfile$chr),
                         ranges = IRanges(start = cytobandfile$start, 
                                          end = cytobandfile$end),
                         stain = cytobandfile$stain, 
                         arm = cytobandfile$arm,
                         band = cytobandfile$band,
                         symbol = cytobandfile$gene_name)
  ## 构建gencodeinfo GRanges
  gencodegr <- GRanges(seqnames = Rle(gencodeinfo$seqnames),
                       ranges = IRanges(start = gencodeinfo$start, 
                                        end = gencodeinfo$end),
                       type = gencodeinfo$gene_type,
                       ensemble = gencodeinfo$gene_id,
                       symbol = gencodeinfo$gene_name)
  ## overlap subsetting
  subs <- subsetByOverlaps(cytobandgr,gencodegr)
  ## get the index
  ovlporder <- match(subs@ranges,cytobandgr@ranges)
  ## merge the symbol
  subs@elementMetadata@listData[["symbol"]] <- gencodegr@elementMetadata@listData[["symbol"]][ovlporder]
  ## band&arm to symbol
  subs[subs@elementMetadata@listData[["arm"]]==arm & subs@elementMetadata@listData[["band"]]==band,"symbol"]
}

试试水：

Chrloc2Sym(cytobandfile = cytobandfile, gencodeinfo = gencodeinfo,arm = "p", band = "36.21")
# GRanges object with 1 range and 1 metadata column:
#       seqnames            ranges strand |   symbol
#                      | 
#   [1]     chr1 12500000-15900000      * |  OR4G11P
#   -------
#   seqinfo: 595 sequences from an unspecified genome; no seqlengths

完美┏ (゜ω゜)=☞

References

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