How to write a data-frame with one column a list to a file?

Question

Here is my dummy dataset:

dataset<-data.frame(a=c(1,2,3,4),b=c('a','b','c','d'), c=c("HI","DD","gg","ff"))
g=list(c("a","b"),c(2,3,4), c(44,33,11,22),c("chr","ID","i","II"))
dataset$l<-g
dataset

 a b  c              l
1 1 a HI           a, b
2 2 b DD        2, 3, 4
3 3 c gg 44, 33, 11, 22
4 4 d ff chr, ID, i, II

> mode(dataset$l)
[1] "list"

when I try to write the dataset to a file:

> write.table(dataset, "dataset.txt", quote=F, sep="\t")
Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec, as.integer(quote),  : 
  unimplemented type 'list' in 'EncodeElement'

How can i solve this problem?

Answer 1

I can think a few options, depending on what you're trying to achieve.

If it is for display only, then you might simply want capture.output() or sink(); neither of these would be very convenient to read back into R:

capture.output(dataset, file="myfile.txt")
### Result is a text file that looks like this:
#   a b  c              l
# 1 1 a HI           a, b
# 2 2 b DD        2, 3, 4
# 3 3 c gg 44, 33, 11, 22
# 4 4 d ff chr, ID, i, II
sink("myfile.txt")
dataset
sink()
## Same result as `capture.output()` approach

If you want to be able to read the resulting table back into R (albeit without preserving the fact that column "l" is a list), you can take an approach similar to what @DWin suggested.

In the code below, the dataset2[sapply... line identifies which variables are lists and concatenates them into a single string. Thus, they become simple character variables, allowing you to use write.table().

dataset2 <- dataset # make a copy just to be on the safe side
dataset2[sapply(dataset2, is.list)] <- apply(dataset2[sapply(dataset2, is.list)], 
                                             1, function(x) 
                                                 paste(unlist(x), 
                                                       sep=", ", collapse=", "))
str(dataset2)
# 'data.frame':    4 obs. of  4 variables:
#  $ a: num  1 2 3 4
#  $ b: Factor w/ 4 levels "a","b","c","d": 1 2 3 4
#  $ c: Factor w/ 4 levels "DD","ff","gg",..: 4 1 3 2
#  $ l: chr  "a, b" "2, 3, 4" "44, 33, 11, 22" "chr, ID, i, II"
write.table(dataset2, "myfile.txt", quote=FALSE, sep="\t")
# can be read back in with: dataset3 <- read.delim("myfile.txt")

Answer 2

Output from save is unreadable. Output from dump or dput is ASCII and is readable to people who understand the structure of R objects, but I'm guessing you wanted it more conventionally arranged.

>  apply(dataset, 1, function(x) paste(x, sep=",", collapse=","))
[1] "1,a,HI,c(\"a\", \"b\")"                  
[2] "2,b,DD,c(2, 3, 4)"                       
[3] "3,c,gg,c(44, 33, 11, 22)"                
[4] "4,d,ff,c(\"chr\", \"ID\", \"i\", \"II\")"

The backslashes do not appear in the text-file output:

 writeLines(con="test.txt", apply(dataset, 1, function(x) paste(x, sep=",", collapse=",")))
#-------output-----
1,a,HI,c("a", "b")
2,b,DD,c(2, 3, 4)
3,c,gg,c(44, 33, 11, 22)
4,d,ff,c("chr", "ID", "i", "II")