一列的组合之间的公共列 [英] common column between combination of one column

问题描述

我有来自分析的数据集。为了解释结果，我正在尝试构建数据帧

结果应如下：

基因名称|Motif_id_1|Motif_id_2|发生|匹配序列

此处某些Motif_id可能共享gene_name，且结果应该是Motif_id的两个组合(允许重叠)。

我尝试了以下代码，但结果未给出Motif_id内的组合。

merge_practice <- reshape2::dcast(group_geneid_CT,
motif_id+ motif_id~gene_name,
value.var ="matched_sequence",
drop = T,fill = 0,
fun.aggregate = length )

如果可能，我希望使其具有内存和时间效率，并减少对包的依赖。有人能给我一个不同的观点吗？

推荐答案

library(tidyverse)

data <- tribble(
  ~gene_name, ~motif_id, ~matched_sequence,
  "A", "y1", "ccc",
  "A", "y2", "ccc",
  "A", "y1", "aaa",
  "A", "y2", "aaa",
  "A", "y2", "aat",
)

data %>%
  pull(motif_id) %>%
  unique() %>%
  combn(2) %>%
  t() %>%
  as_tibble() %>%
  rename(from = V1, to = V2) %>%
  mutate(
    co_occurrence = list(from, to) %>% pmap(~ {
      bind_rows(
        data %>% filter(motif_id == .x) %>% select(-motif_id),
        data %>% filter(motif_id == .y) %>% select(-motif_id)
      ) %>%
        count(gene_name, matched_sequence, name = "co_occurrent")
    })
  ) %>%
  unnest(co_occurrence)
#> Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
#> Using compatibility `.name_repair`.
#> # A tibble: 3 × 5
#>   from  to    gene_name matched_sequence co_occurrent
#>   <chr> <chr> <chr>     <chr>                   <int>
#> 1 y1    y2    A         aaa                         2
#> 2 y1    y2    A         aat                         1
#> 3 y1    y2    A         ccc                         2

^{由reprex package(v2.0.0)}创建于2022-03-01

co_occurrent如果在两个Motif中都找到，则应为2；如果仅在一个Motif中找到，则应为1。

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