当数据连续时，将一些行合并为一行

Question

我有一个 bed file 作为数据帧加载到 R 中。基因组坐标看起来像这样：

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

不需要保留所有行，将其压缩成这样会更好：

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

我怎么可能做到？

我试图用 dplyr 想点什么，但没有成功。 group_by 行不通，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块修改为一个，也因为有很多这样的块。

Answer 1

使用来自 bioconductor 的 GenomicRanges 包，专为床文件等构建：

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)))

当数据连续时，将一些行合并为一行

Merge some rows into one when the data is continuous

r

bioinformatics

dplyr