如何相交并向列添加分数？

Question

我有两个数据集，我想找到它们之间的 overlap/intersect/ 个公共区域，如果有任何重叠，然后提取每个初始 table:

数据A：

   chr  start   end             
 chr1     25     35 
 chr1     50     70   
 chr1     60     85

数据B：

chr     start   end   score               
 chr1     10     15    24
 chr1     55     75    14
 chr1     76     82    10

输出 tables:

out put 1：公共区域的结果

 chr    start   end             
 chr1     55     70   
 chr1     70     75
 chr1     76     82

输出 2：从数据 A 中提取：

 chr    start   end             
 chr1     50     70   
 chr1     60     85

输出 3：从数据 B 中提取：

chr     start   end   score               
 chr1     55     75    14
 chr1     76     82    10

我尝试过不同的方法，但我不知道哪种方法最好：

library(GenomicRanges)
enhancer = with(dataA, GRanges(chr, IRanges(start=start, end=end)))
H3K4me1= with(dataB, GRanges(chr, IRanges(start=start, end=end)))

方式一：

hits <- findOverlaps(dataA, dataB)
ranges(dataA)[queryHits(hits)] = ranges(dataB)[subjectHits(hits)]
dataA
dataB

方式 2:

over<- subsetByOverlaps(dataA, dataB)

方式 3：

inter = intersect(dataA, dataB)

方式 4：

groupA <- data.table(dataA)
setkey(groupA, chr, start, end)

groupB <- data.table(dataB)
setkey(groupB, chr, start, end)

over <- foverlaps(groupA, groupB, nomatch = 0)
over2 <- data.table(
  chr = over$chr,
  start = over[, ifelse(start > i.start, start, i.start)],
  end = over[, ifelse(end < i.end, end, i.end)])

Answer 1

我不确定这是否是您想要的。您介意按照 here.

所述创建一个可重现的示例吗

library(dplyr)

DataA <- data.frame(chr = c("chr1", "chr1", "chr1"), start = c(25,50,60), end = c(35,70,85))
DataB <- data.frame(chr = c("chr1", "chr1", "chr1"), start = c(10,55,76), end = c(15,75,82), score = c(24,14,10))

luA <-  Map(`:`, DataA$start, DataA$end)
luA <- data.frame(value = unlist(luA),
                 index = rep(seq_along(luA), lapply(luA, length)))

DataA[luA$index[match(DataB$start, luA$value)],]
DataB[luA$index[match(DataB$start, luA$value)],]

如何相交并向列添加分数？

how to intersect and add score to column?

intersection

r

overlap

bioconductor