在数据框中将重叠范围合并为唯一的组 [英] Merge overlapping ranges into unique groups, in dataframe

问题描述

我有一个n行3个数据框

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] 开始于178，结束于5025。这与 df $ group [df $ group == 2] ，其起始于983，结束于6918。我想创建一个新列，该列现在将组1和2归为组1（随后将组3归为组2）。 。

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

谢谢您的帮助。

推荐答案

您将需要 IRanges 软件包：

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 ，在R中键入以下行：

To install IRanges, type these lines in R:

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

要了解更多信息（手动等。）转到 此处

To learn more (manual etc..) go here

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