r - 当数据连续时将一些行合并为一行

Question

我有一个bed file它作为数据帧加载到 R 中。基因组坐标如下所示:

chrom   start  end
chrX    400    600
chrX    800    1000
chrX    1000   1200
chrX    1200   1400
chrX    1600   1800
chrX    2000   2200
chrX    2200   2400

没有必要保留所有行，最好将其压缩为这样的内容:

chrom   start  end
chrX    400    600
chrX    800    1400
chrX    1600   1800
chrX    2000   2400

我怎样才能做到这一点？

我尝试用dplyr想出一些东西，但没有成功。 group_by 不起作用，因为我不知道如何使用第一行的起始坐标和最后一行的结束坐标将连续行的 block 修改为一个，也因为有很多这样的 block 。

Answer 1

使用GenomicRanges来自bioconductor的软件包，专门为床文件等构建:

library(GenomicRanges)

# Example data
gr <- GRanges(
  seqnames = Rle("chr1", 6),
  ranges = IRanges(start = c(400 ,800, 1200, 1400, 1800, 2000),
                   end = c(600, 1000, 1400, 1600, 2000, 2200)))
gr
# GRanges object with 6 ranges and 0 metadata columns:
#       seqnames       ranges strand
#          <Rle>    <IRanges>  <Rle>
#   [1]     chr1 [ 400,  600]      *
#   [2]     chr1 [ 800, 1000]      *
#   [3]     chr1 [1200, 1400]      *
#   [4]     chr1 [1400, 1600]      *
#   [5]     chr1 [1800, 2000]      *
#   [6]     chr1 [2000, 2200]      *
#   -------
#   seqinfo: 1 sequence from an unspecified genome; no seqlengths

# merge contiouse ranges into one using reduce:
reduce(gr)
# GRanges object with 4 ranges and 0 metadata columns:
#       seqnames       ranges strand
#          <Rle>    <IRanges>  <Rle>
#   [1]     chr1 [ 400,  600]      *
#   [2]     chr1 [ 800, 1000]      *
#   [3]     chr1 [1200, 1600]      *
#   [4]     chr1 [1800, 2200]      *
#   -------
#   seqinfo: 1 sequence from an unspecified genome; no seqlength

# EDIT: if the bed file is a data.frame we can convert it to ranges object:
gr <- GRanges(seqnames(Rle(df$chrom),
                       ranges = IRanges(start = df$start,
                                        end = df$end)))