在数据框中将重叠范围合并为唯一组 [英] Merge overlapping ranges into unique groups, in dataframe

问题描述

我有一个 n 行和 3 行的数据框

I have a dataframe of n rows and 3

df <- data.frame(start=c(178,400,983,1932,33653),
    end=c(5025,5025, 5535, 6918, 38197),
    group=c(1,1,2,2,3))

df
  start   end group
1   178  5025     1
2   400  5025     1
3   983  5535     2
4  1932  6918     2
5 33653 38197     3

我想创建一个新列 df$group2 将重叠的组重新分类为相同.例如，df$group[df$group==1] 从 178 开始，到 5025 结束.这与 df$group[df$group==2] 重叠，从 983 开始，到 6918 结束.我想创建一个新列，现在将第 1 组和第 2 组分类为第 1 组(随后将第 3 组分类为第 2 组).

I would like to make a new column df$group2 that re-classifies groups that overlap to be the same. For example, df$group[df$group==1] starts at 178 and ends at 5025. This overlaps with df$group[df$group==2], which starts at 983 and ends at 6918. I would like to make a new column that now classifies group 1 and 2 as group 1 (and subsequently, group 3 as group 2).

结果:

df
  start   end group group2
1   178  5025     1      1
2   400  5025     1      1
3   983  5535     2      1
4  1932  6918     2      1
5 33653 38197     3      2

提前感谢您的帮助.

推荐答案

你需要 IRanges 包:

require(IRanges)
ir <- IRanges(df$start, df$end)
df$group2 <- subjectHits(findOverlaps(ir, reduce(ir)))
> df

#  start   end group group2
# 1   178  5025     1      1
# 2   400  5025     1      1
# 3   983  5535     2      1
# 4  1932  6918     2      1
# 5 33653 38197     3      2

要安装 IRanges，请在 R 中输入这些行:

To install IRanges, type these lines in R:

source("http://bioconductor.org/biocLite.R")
biocLite("IRanges")

要了解更多信息(手册等)，请转到 这里

To learn more (manual etc..) go here

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