Question

我有一个bed file作为数据框加载到R.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

没有必要保留所有的行，将它压缩成这样的东西会更好：

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

我怎么可能这样做？

我试图用dplyr来思考但没有成功。 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块修改为一个，因为这些块中有很多。

Answer 1

使用来自bioconductor的GenomicRanges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)))

当数据连续时，将一些行合并为一行

1 个答案: