R-在数据连续时将一些行合并为一行

Question

我有一个床文件，该文件被加载为数据框中的R。基因组坐标，看起来像这样的东西：

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

无需保留所有的行，将其压缩到这样的东西会更好：

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

我该怎么做？

我试图考虑使用dplyr的事情，但没有成功。group_by无法使用，因为我不知道如何使用第一行的启动坐标将连续行的块修改为一个，而从最后一行则结束坐标，因为有许多这些块。

Answer 1

使用BioConductor的Genomicranges软件包，专为床文件等建造：

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)))