CODEWITHSUNDEEP
r
cucurbit
cucurbit

Reputation: 1442

Append list elements to data frame column

I have this dataframe:

       GO.ID Annotated Significant Expected P-value                   Term Ontology
1 GO:0000049         7           0     0.25  1.0000           tRNA binding       MF
2 GO:0000062         4           0     0.14  1.0000 fatty-acyl-CoA binding       MF

And I have this list:

$`GO:0000049`
[1] "Solyc02g090860.2" "Solyc03g119280.2" "Solyc05g056260.2" "Solyc06g048610.2" "Solyc07g008950.2" "Solyc08g015960.2"
[7] "Solyc10g007060.2"

$`GO:0000062`
[1] "Solyc01g099350.2" "Solyc03g082910.2" "Solyc04g078090.2" "Solyc08g075690.2"

Is there any way to print the elements of the list to a new column of the data frame? The order is the same in both structures, I mean, the GO.ID column is ordered as the list elements. I'm looking for something like paste bash command.

I've tried lapply and export the list to a file. Then write.table with the dataframe and then paste command in bash. But I'm wondering if there is a way to do this kind of job in R.

And yes, I'm newbie to R world.

EDIT:

This is my desired output:

       GO.ID Annotated Significant Expected P-value                   Term Ontology           Gene_ID
1 GO:0000049         7           0     0.25  1.0000           tRNA binding       MF           Solyc02g090860.2,Solyc03g119280.2,Solyc05g056260.2,Solyc06g048610.2,Solyc07g008950.2,Solyc08g015960.2,Solyc10g007060.2
2 GO:0000062         4           0     0.14  1.0000 fatty-acyl-CoA binding       MF           Solyc01g099350.2,Solyc03g082910.2,Solyc04g078090.2,Solyc08g075690.2

Upvotes: 3

Views: 5586

Answers (2)

Anton
Anton

Reputation: 3036

(I apologise for using dplyr here. All of this can be done using built-in R functions but I don't remember the last time I used them)

library(dplyr)
library(tidyr)

# sample data
l <- list("GO.0000049" = c(1,2,3), "GO:0000062" = c(4,5,6))
df <- data.frame(GO.ID = c("GO.0000049", "GO:0000062"), Annotated = c(7,4), stringsAsFactors = F)

# actual magic
result <- gather(as_data_frame(lapply(l, function(x) paste(x, collapse=","))), "GO.ID", "Gene_ID") %>% inner_join(df)

And your result would be:

Source: local data frame [2 x 3]

       GO.ID Gene_ID Annotated
1 GO.0000049   1,2,3         7
2 GO:0000062   4,5,6         4

Upvotes: 2

Colonel Beauvel
Colonel Beauvel

Reputation: 31161

If df is your data.frame and lst your list, you can do:

transform(df, Gene_ID=sapply(lst, paste0, collapse=',')[GO.ID])

Upvotes: 6

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