How to convert list of list into a tibble (dataframe)

Question

I have the following list of list. It contains two variables: pair and genes. The contain of pair is always vector with two strings. And the variable genes is a vector which can contain more than 1 values.

lol <- list(structure(list(pair = c("BoneMarrow", "Pulmonary"), genes = "PRR11"), .Names = c("pair", 
"genes")), structure(list(pair = c("BoneMarrow", "Umbilical"), 
    genes = "GNB2L1"), .Names = c("pair", "genes")), structure(list(
    pair = c("Pulmonary", "Umbilical"), genes = "ATP1B1"), .Names = c("pair", 
"genes")))


lol
#> [[1]]
#> [[1]]$pair
#> [1] "BoneMarrow" "Pulmonary" 
#> 
#> [[1]]$genes
#> [1] "PRR11"
#> 
#> 
#> [[2]]
#> [[2]]$pair
#> [1] "BoneMarrow" "Umbilical" 
#> 
#> [[2]]$genes
#> [1] "GNB2L1"
#> 
#> 
#> [[3]]
#> [[3]]$pair
#> [1] "Pulmonary" "Umbilical"
#> 
#> [[3]]$genes
#> [1] "ATP1B1"

How can I convert it into this dataframe:

pair1         pair2        genes_vec
BoneMarrow    Pulmonary    PRR11
BoneMarrow    Umbilical    GNB2L1
Pulmonary     Umbilical    ATP1B1

Note that the genes variable is a vector not single string.

My best try is this which doesn't give what I want:

> do.call(rbind, lapply(lol, data.frame, stringsAsFactors=FALSE))
        pair  genes
1 BoneMarrow  PRR11
2  Pulmonary  PRR11
3 BoneMarrow GNB2L1
4  Umbilical GNB2L1
5  Pulmonary ATP1B1
6  Umbilical ATP1B1

Update:

With new example to show vector content of genes

lol2 <- list(structure(list(pair = c("BoneMarrow", "Pulmonary"), genes = c("GNB2L1", 
"PRR11")), .Names = c("pair", "genes")), structure(list(pair = c("BoneMarrow", 
"Umbilical"), genes = "GNB2L1"), .Names = c("pair", "genes")), 
    structure(list(pair = c("Pulmonary", "Umbilical"), genes = "ATP1B1"), .Names = c("pair", 
    "genes")))

lol2
#> [[1]]
#> [[1]]$pair
#> [1] "BoneMarrow" "Pulmonary" 
#> 
#> [[1]]$genes
#> [1] "GNB2L1" "PRR11" 
#> 
#> 
#> [[2]]
#> [[2]]$pair
#> [1] "BoneMarrow" "Umbilical" 
#> 
#> [[2]]$genes
#> [1] "GNB2L1"
#> 
#> 
#> [[3]]
#> [[3]]$pair
#> [1] "Pulmonary" "Umbilical"
#> 
#> [[3]]$genes
#> [1] "ATP1B1"

The expected output is:

pair1         pair2        genes_vec
BoneMarrow    Pulmonary    PRR11,GNB2L1
BoneMarrow    Umbilical    GNB2L1
Pulmonary     Umbilical    ATP1B1

user_2473891 · Answer

For the first question, pretty much the same as other answers, slightly shorter/more compact:

library(tidyverse)
lol <- list(structure(list(pair = c("BoneMarrow", "Pulmonary"), genes = "PRR11"),
                      .Names = c("pair", "genes")),
            structure(list(pair = c("BoneMarrow", "Umbilical"), genes = "GNB2L1"),
                      .Names = c("pair", "genes")),
            structure(list(pair = c("Pulmonary", "Umbilical"), genes = "ATP1B1"), .Names = c("pair","genes")))


map_dfr(lol, ~as_tibble(.) %>% 
          mutate(row=paste0("pair", row_number()))%>% 
          spread(row, pair) %>% 
          select(pair1, pair2, genes))
#> # A tibble: 3 x 3
#>   pair1      pair2     genes 
#>               
#> 1 BoneMarrow Pulmonary PRR11 
#> 2 BoneMarrow Umbilical GNB2L1
#> 3 Pulmonary  Umbilical ATP1B1

^{Created on 2020-12-04 by the reprex package (v0.3.0)}

How to convert list of list into a tibble (dataframe)

5 Answers