Data frame to a nested list in R
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bbhatt • 0
@a2a4910b
Last seen 2.4 years ago
Canada

Hi, I have a question regarding converting the data frame to a nested list in R. I have a data frame as shown in the screenshot below wherein column 1 depicts the Ensembl IDs and column 2 are the miRNAs.

data frame with Ensembl IDs (redundant, in column 1) and miRNAs in column2

Now, I want to convert this data frame to a nested list such that the redundancy in column 1 (i.e., Ensembl IDs) is removed and the list looks something like this as follows:

nested list without redundacy

It would be really great if you can please provide any suggestions or recommendations to accomplish this in R. Thanks very much!

RBioinf • 3.4k views
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Quite simply, you can use the nest function. This will create a column that contains a tibble for the data associated with each ID.

Sometimes it's handy to have that list column in a different form, such as an array or a JSON string (e.g. including in a database). Alternatively, you may want the data in a list as opposed to a tibble.

Here are some examples:

library(tidyverse)
library(jsonlite)
#> 
#> Attaching package: 'jsonlite'
#> The following object is masked from 'package:purrr':
#> 
#>     flatten

tb = tibble(A = c("a", "a", "a", "b", "b", "b", "b", "c"), B = letters[1:8])

tb
#> # A tibble: 8 x 2
#>   A     B    
#>   <chr> <chr>
#> 1 a     a    
#> 2 a     b    
#> 3 a     c    
#> 4 b     d    
#> 5 b     e    
#> 6 b     f    
#> 7 b     g    
#> 8 c     h

tb_nested = tb %>% nest(B = B)

tb_nested %>% pull(B)
#> [[1]]
#> # A tibble: 3 x 1
#>   B    
#>   <chr>
#> 1 a    
#> 2 b    
#> 3 c    
#> 
#> [[2]]
#> # A tibble: 4 x 1
#>   B    
#>   <chr>
#> 1 d    
#> 2 e    
#> 3 f    
#> 4 g    
#> 
#> [[3]]
#> # A tibble: 1 x 1
#>   B    
#>   <chr>
#> 1 h

tb_nested_json =
  tb_nested %>%
  rowwise() %>%
  mutate(B = toJSON(B))

tb_nested_json
#> # A tibble: 3 x 2
#> # Rowwise: 
#>   A     B                                        
#>   <chr> <json>                                   
#> 1 a     [{"B":"a"},{"B":"b"},{"B":"c"}]          
#> 2 b     [{"B":"d"},{"B":"e"},{"B":"f"},{"B":"g"}]
#> 3 c     [{"B":"h"}]

tb_nested_list =
  tb_nested %>%
  rowwise() %>%
  mutate(B = list(pull(B, B)))

tb_nested_list %>% pull(B)
#> [[1]]
#> [1] "a" "b" "c"
#> 
#> [[2]]
#> [1] "d" "e" "f" "g"
#> 
#> [[3]]
#> [1] "h"

tb_nested_list %>%
  filter(A == "a") %>%
  pull(B)
#> [[1]]
#> [1] "a" "b" "c"

tb_nested_list %>%
  rowwise() %>%
  mutate(B = toJSON(B))
#> # A tibble: 3 x 2
#> # Rowwise: 
#>   A     B                
#>   <chr> <json>           
#> 1 a     ["a","b","c"]    
#> 2 b     ["d","e","f","g"]
#> 3 c     ["h"]

tb_nested_string =
  tb_nested %>%
  rowwise() %>%
  mutate(B = paste0(c_across(B)[[1]], collapse="|"))

tb_nested_string
#> # A tibble: 3 x 2
#> # Rowwise: 
#>   A     B      
#>   <chr> <chr>  
#> 1 a     a|b|c  
#> 2 b     d|e|f|g
#> 3 c     h

Created on 2021-12-12 by the [reprex package](https://reprex.tidyverse.org) (v2.0.1)

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Hi Ariel, thanks very much for responding. I really appreciate it. Have a good one!

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Mike Smith ★ 6.5k
@mike-smith
Last seen 5 hours ago
EMBL Heidelberg

Ariel's answer look great and very comprehensive. If you want to stick to base R and data.frames you can use the split() function e.g.

df = data.frame(A = c("a", "a", "a", "b", "b", "b", "b", "c"), B = letters[1:8])
split(df$B, df$A)
#> $a
#> [1] "a" "b" "c"
#> 
#> $b
#> [1] "d" "e" "f" "g"
#> 
#> $c
#> [1] "h"
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Well, the OP did ask for a nested list, so YOUR answer is probably the better one :)

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It worked fine. Thanks! :)

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Hi Mike, thanks very much for responding. I really appreciate your help. Have a good one!

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