如何计算R中的重叠百分比 [英] How to compute percentage of overlap in R

问题描述

我正在尝试计算满足某些标准的两个具有基因组坐标的数据集之间的重叠百分比。

Seg2

ID   chrom loc.start   loc.end num.mark seg.mean
AB    1   3010000 173490000     8430   0.0039
AB    1 173510000 173590000        5  -17.738
AB    1 173610000 173830000       12    0.011
AB    1 173850000 173970000        6  -16.121
AB    2   3090000 181990000     8434    0.011
BB   12   3090000  68990000     2950   -0.2022
BB   12  69010000  87790000      889    0.0267
BB   12  88010000  98550000      507   -0.3337
BB   12  98570000 115090000      800    0.0586
BB   12 115110000 119350000      197   -0.2031
BB   12 119370000 119430000        4   -20.671

超过

 chr     start   end    CNA      sample.ID
  1  68580000  68640000 loss    1-68580000-68640000
  3  15360000  16000000 loss    3-15360000-16000000
  4 122660000 123500000 gain   4-122660000-123500000
  7  48320000  48400000 loss    7-48320000-48400000
  12 115860000 115980000 loss  12-115860000-115980000
 12 113560000 114920000 gain   12-113560000-114920000

预期产量

ID   chrom loc.start   loc.end num.mark seg.mean  lm(percentage of overlap)
AB    1   3010000 173490000     8430   0.0039         %
AB    1 173510000 173590000        5  -17.738     
AB    1 173610000 173830000       12    0.011     
AB    1 173850000 173970000        6  -16.121     
AB    2   3090000 181990000     8434    0.011     
BB   12   3090000  68990000     2950   -0.2022     
BB   12  69010000  87790000      889    0.0267
BB   12  88010000  98550000      507   -0.3337
BB   12  98570000 115090000      800    0.0586
BB   12 115110000 119350000      197   -0.2031
BB   12 119370000 119430000        4   -20.671

我尝试了此脚本，但它不起作用。

for (i in 1:now(seg2)) { 
    seg2$lm <- if((seg2$chrom[i] == over$chr[i]) |
    (seg2$loc.start[i] <= over$start[i] & seg2$loc.end[i] >= over$end[i]) |
    (over$seg.mean[i] >= 0.459 & seg2$CNA[i] == "gain") |
    (over$seg.mean[i] <= -0.678 & seg2$CNA[i] == "loss"), 
    (over$end[i]-over$start[i])/(seg2$loc.end[i]-seg2$loc.start[i])*100)
    }

我知道GenomicRanges包，但非常感谢您的建议。

推荐答案

我强烈建议您使用GenomicFeatures来高效地完成此操作。如果您已经知道要创建自己的Granges对象，则需要执行以下两个步骤来获取重叠长度

# to find overlaps
overlappin.index = findOverlaps(object1, object2)

# to get the overlap length 
width(ranges(overlapping.index, ranges(object1),ranges(object2)))

其中，对象1和对象2是有坐标的GRanges对象，重叠对象的索引。 一旦您有了长度，您就可以很容易地获得百分比。

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