查找重叠区域并提取各自的值

问题描述

如何找到重叠的坐标并提取重叠区域的相应seg.mean值?

How do you find the overlapping coordinates and extract the respective seg.mean values for the overlapping region?

data1
      Rl       pValue     chr  start    end     CNA
      2        2.594433   6 129740000 129780000 gain
      2        3.941399   6 130080000 130380000 gain
      1        1.992114  10  80900000  81100000 gain
      1        7.175750  16  44780000  44920000 gain

data2

ID     chrom   loc.start   loc.end   num.mark  seg.mean
8410     6     129750000  129760000      8430   0.0039
8410     10    80907000   81000000        5   -1.7738
8410     16    44790000   44910000       12    0.0110

数据输出

  Rl       pValue     chr  start    end        CNA    seg.mean
  2        2.594433   6 129750000   129760000  gain   0.0039
  1        1.992114  10  80907000   81000000   gain   -1.7738
  1        7.175750  16  44790000   44910000   gain   0.0110

推荐答案

在使用基因组数据时，将数据保留为Granges对象更加容易，那么我们可以使用GenomicRanges包中的-mergeByOverlaps(g1,g2)，请参见下文例如:

As we are working with genomics data it is easier to keep data as Granges objects, then we could use - mergeByOverlaps(g1,g2) from GenomicRanges package, see below example:

library("GenomicRanges")

#data
x1 <- read.table(text="Rl       pValue     chr  start    end     CNA
      2        2.594433   6 129740000 129780000 gain
      2        3.941399   6 130080000 130380000 gain
      1        1.992114  10  80900000  81100000 gain
      1        7.175750  16  44780000  44920000 gain",header=TRUE)

x2 <- read.table(text="ID     chrom   loc.start   loc.end   num.mark  seg.mean
8410     6     129750000  129760000      8430   0.0039
8410     10    80907000   81000000        5   -1.7738
8410     16    44790000   44910000       12    0.0110",header=TRUE)

g1 <-  GRanges(seqnames=paste0("chr",x1$chr),
               IRanges(start=x1$start,
                       end=x1$end),
               CNA=x1$CNA,
               Rl=x1$Rl)


g2 <-  GRanges(seqnames=paste0("chr",x2$chrom),
               IRanges(start=x2$loc.start,
                       end=x2$loc.end),
               ID=x2$ID,
               num.mark=x2$num.mark,
               seq.mean=x2$seg.mean)

mergeByOverlaps(g1,g2)
# DataFrame with 3 rows and 7 columns
#                               g1      CNA        Rl                             g2        ID  num.mark  seq.mean
#                        <GRanges> <factor> <integer>                      <GRanges> <integer> <integer> <numeric>
# 1  chr6:*:[129740000, 129780000]     gain         2  chr6:*:[129750000, 129760000]      8410      8430    0.0039
# 2 chr10:*:[ 80900000,  81100000]     gain         1 chr10:*:[ 80907000,  81000000]      8410         5   -1.7738
# 3 chr16:*:[ 44780000,  44920000]     gain         1 chr16:*:[ 44790000,  44910000]      8410        12    0.0110

---

添加了sessionInfo()输出:

---

Added sessionInfo() output:

R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GenomicRanges_1.20.3 GenomeInfoDb_1.4.0   IRanges_2.2.1        S4Vectors_0.6.0      BiocGenerics_0.14.0
[6] BiocInstaller_1.18.1

loaded via a namespace (and not attached):
[1] XVector_0.8.0 tools_3.2.0

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