Collating or alternately merging two columns into one list in R

Question

Is there an easy way to alternately merge two columns into one list/dataframe column in R? Essentially I need to do a large series of manipulation of genetic data, sorting etc... and eventually I am left with an identifier and a sequence. What is the easiest way to create a single list that has each identifier above its sequence in a single list?

I have data: df <- data.frame(genenames = c("gene1", "gene2", "gene3"), seqnes = c("gattaca", "gatgatcca", "catgatcat"))

I would like to get to: data.frame(c("gene1", "gattaca", "gene2","gatgatcca", "gene3", "catgatcat"))

using either unite(data, "identifier", "sequence", sep = " ") will result in all data fuse within a single column as well as stack(......)

Is there an easy or elegant way to do this save starting to look into writing a small loop to iteratively write out the new list?

Possible duplicate https://stackoverflow.com/questions/31989270/unlist-a-data-frame-by-rows-not-columns — Ronak Shah, Sep 24 '19 at 13:52

score 2 · Answer 1 · answered Sep 24 '19 at 13:30

2

Is this what you want?

> data.frame("wut"=unname(unlist(data.frame(t(df)))))
        wut
1     gene1
2   gattaca
3     gene2
4 gatgatcca
5     gene3
6 catgatcat

answered Sep 24 '19 at 13:30

user2974951

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slava-kohut · Answer 2 · 2019-09-24T17:28:52.763

2

Elegant one-liner. No column specs and loops are needed.

df <- data.frame(new_col = c(t(df)))

edited Sep 24 '19 at 17:28

answered Sep 24 '19 at 13:34

slava-kohut

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score 1 · Accepted Answer · answered Sep 24 '19 at 13:29

1

Here is one potential solution with gather from tidyrand some dplyr

library(dplyr)
library(tidyr)

df %>%
  mutate(obs = 1:nrow(df)) %>%
  gather(identifier, sequence, -obs) %>%
  arrange(obs, desc(identifier))

answered Sep 24 '19 at 13:29

Bjørn Kallerud

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8
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score 0 · Answer 4 · answered Sep 24 '19 at 13:35

0

Making a list:

lapply(apply(df, 1, identity), unlist)

answered Sep 24 '19 at 13:35

Christoffer Sannes

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Collating or alternately merging two columns into one list in R

4 Answers4