R-从多个列中检索特定信息

我有一个巨大的数据框

df

，其中包括关于重叠间隔（a）和（B）以及它们位于哪个染色体（chrom）上的信息。还有关于间隔（a）内观察到的值（基因表达水平）的信息

请注意，相同的间隔可能出现多次，例如，如果间隔（B）与两个（A）间隔重叠，则会报告两次：

Astart(1)=========================Aend1    Astart(2)========================Aend(2)
          Bstart(1)=======================================Bend(1)

chrom value Astart   Aend  Bstart  Bend
chr1      0      0     25      15    35    #A(1) and B(1) overlap
chr1      1     28     45      15    35    #A(2) and B(1) overlap

同样，如果间隔（A）与两个或多个（B）间隔重叠，则间隔（A）将被报告两次或多次：

Astart(3)===================================================================Aend(3)
          Bstart(2)=========Bend(2)  Bstart(3)===========Bend(3) Bstart(4)===============Bend(4)

chrom value Astart   Aend  Bstart  Bend
chr4      0     10    100      15    25    #A(3) and B(2) overlap
chr4      0     10    100      30    75    #A(3) and B(3) overlap
chr4      3     10    100      80   120    #A(3) and B(4) overlap

我的目标是输出间隔（B）中的所有单个位置和（A）中的相应值。我有一段代码，漂亮地输出了（B）中的所有相关位置：

---

调用

ddply

可能更优雅，但逻辑相同：

dfA = read.table(textConnection("chrom value    Astart      Aend    Bstart      Bend
 chr1     0         0  54519752     17408     17431
 chr1     0         0  54519752     17368     17391
 chr1     0         0  54519752    567761    567783
chr11     0         2  93466832    568111    568133
chr11     0         2  93466832    568149    568171
chr11     0         2  93466832   1880734   1880756
chr11     4  93466844  93466880  93466856  93466878
chr11     2  93466885 135006516  93466889  93466911
chr11     2  93466885 135006516  94199710  94199732"), header = TRUE)


dfB = as.data.frame(do.call(rbind, 
        apply(dfA, MARGIN = 1,  FUN = function(x) {
          cbind(mapply(seq, 
                       as.numeric(x['Bstart']),
                       as.numeric(x['Bend']) - 1),
                x['chrom'], x['value'])
        }
        )))
lapply(dfB, typeof)

---

谢谢你结束了48小时的挫折！！：DDo您知道我如何避免在“”之间获取所有输出值吗？@biohadise只需将整个内容包装在一个

as.data.frame

中。

position <- unlist(mapply(seq, ans$Bstart, ans$Bend - 1))
> head(position)
[1] 17408 17409 17410 17411 17412 17413

> head(expected_result)
chrom    position   value
chr1     17408      0
chr1     17409      0
chr1     17410      0
chr1     17411      0
chr1     17412      0
chr1     17413      0
#skipping some lines to show another part of the dataframe
chr11    93466856   4
chr11    93466857   4

dfA = read.table(textConnection("chrom value    Astart      Aend    Bstart      Bend
 chr1     0         0  54519752     17408     17431
 chr1     0         0  54519752     17368     17391
 chr1     0         0  54519752    567761    567783
chr11     0         2  93466832    568111    568133
chr11     0         2  93466832    568149    568171
chr11     0         2  93466832   1880734   1880756
chr11     4  93466844  93466880  93466856  93466878
chr11     2  93466885 135006516  93466889  93466911
chr11     2  93466885 135006516  94199710  94199732"), header = TRUE)


dfB = as.data.frame(do.call(rbind, 
        apply(dfA, MARGIN = 1,  FUN = function(x) {
          cbind(mapply(seq, 
                       as.numeric(x['Bstart']),
                       as.numeric(x['Bend']) - 1),
                x['chrom'], x['value'])
        }
        )))
lapply(dfB, typeof)