查找重叠区域并提取各自的值 [英] Find overlapping regions and extract respective value

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  

这篇关于查找重叠区域并提取各自的值的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！