在GenomicRanges对象中合并具有相同属性的相邻箱

Question

在将基因组分割成相邻的不重叠的bin之后，例如通过tileGenome，我已经通过某种方法为每个bin(例如1或2)计算了一些属性。

现在，我想合并具有相同属性的相邻对象。下面是一个最小的例子：

library(GenomicRanges)
chrSizes <- c(chr1 = 1000, chr2 = 500)
bins   <- tileGenome(chrSizes, tilewidth = 200, cut.last.tile.in.chrom = T)
bins$property <- rep(1:2, each = 4)
bins
GRanges object with 8 ranges and 1 metadata column:
      seqnames    ranges strand |  property
         <Rle> <IRanges>  <Rle> | <integer>
  [1]     chr1     1-200      * |         1
  [2]     chr1   201-400      * |         1
  [3]     chr1   401-600      * |         1
  [4]     chr1   601-800      * |         1
  [5]     chr1  801-1000      * |         2
  [6]     chr2     1-200      * |         2
  [7]     chr2   201-400      * |         2
  [8]     chr2   401-500      * |         2
  -------
  seqinfo: 2 sequences from an unspecified genome

前4个bin的属性为1，因此应该合并到一个bin中。

我浏览了GRanges文档，但找不到明显的本机解决方案。请注意，必须考虑seqname边界(例如，无论属性如何，chr1和chr2保持分离)显然，我可以使用循环，但我更喜欢使用原生GRange解决方案，例如使用我可能会监督的union。

所需的输出应如下所示：

      seqnames    ranges strand |  property
         <Rle> <IRanges>  <Rle> | <integer>
  [1]     chr1     1-800      * |         1
  [2]     chr1  801-1000      * |         2
  [3]     chr2     1-500      * |         2

Answer 1

R GenomicRanges：

result <- unlist(reduce(split(bins, ~property)))
result$property <- names(result)

# GRanges object with 3 ranges and 1 metadata column:
# seqnames    ranges strand |    property
# <Rle> <IRanges>  <Rle> | <character>
# 1     chr1     1-800      * |           1
# 2     chr1  801-1000      * |           2
# 2     chr2     1-500      * |           2
# -------
# seqinfo: 2 sequences from an unspecified genome

Python PyRanges：

import pandas as pd
from io import StringIO
import pyranges as pr

c = """Chromosome Start End Value
chr1 1 200 Python
chr1 201 400 Python
chr1 401 600 Python
chr1 601 800 Python
chr1 801 1000 R
chr2 1 200 R
chr2 201 400 R
chr2 401 500 R"""

df = pd.read_table(StringIO(c), sep=" ")
gr = pr.PyRanges(df)
gr.merge(by="Value", slack=1)

# +--------------+-----------+-----------+------------+
# | Chromosome   |     Start |       End | Value      |
# | (category)   |   (int32) |   (int32) | (object)   |
# |--------------+-----------+-----------+------------|
# | chr1         |         1 |       800 | Python     |
# | chr1         |       801 |      1000 | R          |
# | chr2         |         1 |       500 | R          |
# +--------------+-----------+-----------+------------+
# Unstranded PyRanges object has 3 rows and 4 columns from 2 chromosomes.
# For printing, the PyRanges was sorted on Chromosome.