在 summarize() 中提取匹配变量

Question

我有一个示例数据集

gene_name	motif_id	matched_sequence
A	y1	CCC
A	y2	CCAAA
A	y3	AAG
A	y3	AT
B	y1	AAAA
B	y4	AAT
C	y5	AAGG

并尝试像 R 中那样获取数据集：

gene_name	Node1	Node2	sequence	occurence
A	y1	y2	CCC, CCAAA	2
A	y1	y3	CCC,AAG,AAT	3
A	y2	y3	CCAAA,AGG,AAT	3
B	y1	y4	AAAA,AAT	2

motif_id 列总是有一个目标并从起始列的每个组合中寻找常见的 gene_name没有任何重叠及其序列列表。

我试过了:

data%>% 
  group_by(gene_name, motif_id) %>% 
  summarize(matched_sequence = paste0(matched_sequence, collapse = ",")) %>% 
  mutate(count = n()) %>% filter(count>=2) %>%
  summarize(motif_id = combn(motif_id, 2, function(x) list(setNames(x, c('Node1', 'Node2')))), matched_sequence = toString(matched_sequence),
            .groups = 'keep') %>%
  tidyr::unnest_wider(motif_id)

但是无法获取序列和出现列。谁能给我一个建议？

Answer 1

我们按 'gene_name' 进行分组，仅保留 'motif_id' 中不同（n_distinct 元素的数量大于 1 的组。得到成对的 combnations 'unique' 元素，通过提取与 'motif_id' 值匹配的 'matched_sequence' 创建 'sequence'，获取 list 中的 lengths 'occurence'，使用 unnest_wider 从 list 列创建列，并通过 pasteing 将 'sequence' list 转换为 character 列list

中的元素

library(dplyr)
library(purrr)
library(tidyr)
library(stringr)
data %>%
   dplyr::group_by(gene_name) %>%  
   dplyr::filter(n() > 1, n_distinct(motif_id) > 1) %>% 
   dplyr::summarise(Node =  combn(unique(motif_id), 2, 
       simplify = FALSE),
    sequence = purrr::map(Node, ~ 
        matched_sequence[motif_id  %in% .x]),
     occurence = lengths(sequence), .groups = 'drop') %>%
   tidyr::unnest_wider(Node) %>%
   dplyr::mutate(sequence = purrr::map_chr(sequence, toString)) %>%
   dplyr::rename_with(~ stringr::str_c("Node", seq_along(.x)), starts_with("..."))

-输出

# A tibble: 4 × 5
  gene_name Node1 Node2 sequence       occurence
  <chr>     <chr> <chr> <chr>              <int>
1 A         y1    y2    CCC, CCAAA             2
2 A         y1    y3    CCC, AAG, AT           3
3 A         y2    y3    CCAAA, AAG, AT         3
4 B         y1    y4    AAAA, AAT              2

数据

data <- structure(list(gene_name = c("A", "A", "A", "A", "B", "B", "C"
), motif_id = c("y1", "y2", "y3", "y3", "y1", "y4", "y5"), 
matched_sequence = c("CCC", 
"CCAAA", "AAG", "AT", "AAAA", "AAT", "AAGG")), 
class = "data.frame", row.names = c(NA, 
-7L))

在 summarize() 中提取匹配变量

extracting matching variable in summarize()

r

function

data-manipulation

dplyr

summarize

数据