在R中获取两个文件之间的交集

Question

我有人类外显子的位置(染色体数目，外显子开始和外显子末端)

> head(a1)
        exon Chromosome Start   End
1 uc001aaa.3          1 11873 12227
2 uc001aaa.3          1 12612 12721
3 uc001aaa.3          1 13220 14409
4 uc010nxr.1          1 11873 12227
5 uc010nxr.1          1 12645 12697
6 uc010nxr.1          1 13220 14409
> str(a)
'data.frame':   8 obs. of  4 variables:
 $ exon      : chr  "uc001aaa.3" "uc001aaa.3" "uc001aaa.3" "uc010nxr.1" ...
 $ Chromosome: int  1 1 1 1 1 1 1 1
 $ Start     : int  11873 12612 13220 11873 12645 13220 11873 12594
 $ End       : int  12227 12721 14409 12227 12697 14409 12227 12721
> dput(a)
structure(list(exon = c("uc001aaa.3", "uc001aaa.3", "uc001aaa.3", 
"uc010nxr.1", "uc010nxr.1", "uc010nxr.1", "uc010nxq.1", "uc010nxq.1"
), Chromosome = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), Start = c(11873L, 
12612L, 13220L, 11873L, 12645L, 13220L, 11873L, 12594L), End = c(12227L, 
12721L, 14409L, 12227L, 12697L, 14409L, 12227L, 12721L)), class = "data.frame", row.names = c(NA, 
-8L))
>

我有另一份文件

  > head(a2)
  SampleID Chromosome    Start      End
1  sampel1          1    64613  5707515
2  sampel1          1  5712940  5732322
3  sampel1          1  5732399 16383682
4  sampel1          1 16383742 16389288
5  sampel1          1 16390813 16830026
6  sampel1          1 16830201 17278112
> str(a2)
'data.frame':   7 obs. of  4 variables:
 $ SampleID  : chr  "sampel1" "sampe1" "sampel1" "sampel1" ...
 $ Chromosome: int  1 1 1 1 1 1 1
 $ Start     : int  64613 5712940 5732399 16383742 16390813 16830201 17284498
 $ End       : int  5707515 5732322 16383682 16389288 16830026 17278112 120374803
> dput(a2)
structure(list(SampleID = c("sampel1", "sampe1", "sampel1", "sampel1", 
"sampel1", "sampel1", "sampel1"), Chromosome = c(1L, 1L, 1L, 
1L, 1L, 1L, 1L), Start = c(64613L, 5712940L, 5732399L, 16383742L, 
16390813L, 16830201L, 17284498L), End = c(5707515L, 5732322L, 
16383682L, 16389288L, 16830026L, 17278112L, 120374803L)), class = "data.frame", row.names = c(NA, 
-7L))
>

我想知道在第二个文件的间隔中有多少外显子。

在第二个文件中，假设64613到5707515中有多少外显子

我的欲望输出就像

​

​

Answer 1

您正在寻找GenomicRanges包：

library(GenomicRanges)
a1.GRanges <- GRanges(a1$Chromosome,
                         ranges = IRanges(a1$Start, a1$End),
                         seqinfo = a1$exons)

a2.GRanges <- GRanges(a2$Chromosome,
                                ranges = IRanges(a2$Start, a2$End),
                                seqinfo = a2$SampleID)

findOverlaps(a2.GRanges,a1.GRanges)

正如@A5C1D2H2I1M1N2O1R2T1所暗示的那样，在这些范围内没有重叠。