如何有效地找到序列坐标inn R的两个数据表之间的重叠？答案

【问题标题】：How to efficiently find the overlap between two data tables of sequence coordinates inn R?如何有效地找到序列坐标inn R的两个数据表之间的重叠？
【发布时间】：2020-10-23 17:21:49
【问题描述】：

我有两个带有不同序列坐标的大型数据表。例如：

library(data.table)

dt1 <- data.table(cat = c(rep("A", 2), rep("B", 2)),
                  start = c(1, 4, 2, 15),
                  end = c(6, 9, 5, 20))
dt2 <- data.table(cat = c(rep("A", 2), rep("B", 2)),
                  start = c(2, 1, 10, 17),
                  end = c(7, 3, 12, 20))

我需要为重叠序列创建一个坐标数据表（即每个类别的两个数据表中给出的序列中出现的整数）。我目前可以使用 for 循环来做到这一点。例如：

seq2 <- Vectorize(seq.default, vectorize.args = c("from", "to"))
out_list <- list()
for(i in 1:length(unique(dt1$cat))){
  sub1 <- dt1[cat == unique(dt1$cat)[i]]
  sub2 <- dt2[cat == unique(dt1$cat)[i]]
  vec1 <- unique(unlist(c(seq2(from = sub1$start, to = sub1$end))))
  vec2 <- unique(unlist(c(seq2(from = sub2$start, to = sub2$end))))
  
  vec <- Reduce(intersect, list(vec1, vec2))
  
  vec_dt <- data.table(V1 = vec)
    output <- vec_dt[order(V1), 
                     .(start = min(V1),
                       end = max(V1)),
                     by = .(grp = rleid(c(0, cumsum(diff(V1) > 1))))
                     ]
    output$grp <- NULL
    output$cat <- unique(dt1$cat)[i]
  out_list[[i]] <- output
  print(i)
}
output_dt <- do.call("rbind", out_list)

但是，我需要应用它的数据集非常大（无论是行数还是向量的大小）。有没有人能提出提高性能的方法？

谢谢

【问题讨论】：

标签： r performance data.table sequence

【解决方案1】：

您可以 (a) 将开始/结束变量转换为序列，(b) 进行内部连接，(c) 转换回开始/结束。

library(data.table)

dt1 <- data.table(cat = c(rep("A", 2), rep("B", 2)),
                  start = c(1, 4, 2, 15),
                  end = c(6, 9, 5, 20))
dt2 <- data.table(cat = c(rep("A", 2), rep("B", 2)),
                  start = c(2, 1, 10, 17),
                  end = c(7, 3, 12, 20))

# convert to sequence
dt1 = dt1[, .(sequence = start:end), by=.(cat, 1:nrow(dt1))][
          , nrow := NULL]
dt2 = dt2[, .(sequence = start:end), by=.(cat, 1:nrow(dt2))][
          , nrow := NULL]

# inner join + unique
overlap = merge(dt1, dt2)
overlap = unique(overlap)

# convert to start/end
overlap = overlap[, .(start=min(sequence), end=max(sequence)), by=.(cat)]

# result
overlap
#>    cat start end
#> 1:   A     1   7
#> 2:   B    17  20

【讨论】：