R: convert data.frame columns from factors to characters

Question

Hi,

I have a data frame. Let's call him bob:

> head(bob)
                 phenotype                         exclusion
GSM399350 3- 4- 8- 25- 44+ 11b- 11c- 19- NK1.1- Gr1- TER119-
GSM399351 3- 4- 8- 25- 44+ 11b- 11c- 19- NK1.1- Gr1- TER119-
GSM399352 3- 4- 8- 25- 44+ 11b- 11c- 19- NK1.1- Gr1- TER119-
GSM399353 3- 4- 8- 25+ 44+ 11b- 11c- 19- NK1.1- Gr1- TER119-
GSM399354 3- 4- 8- 25+ 44+ 11b- 11c- 19- NK1.1- Gr1- TER119-
GSM399355 3- 4- 8- 25+ 44+ 11b- 11c- 19- NK1.1- Gr1- TER119-

I'd like to concatenate the rows of this data frame (this will be another question). But look:

> class(bob$phenotype)
[1] "factor"

Bob's columns are factors. So, for example:

> as.character(head(bob))
[1] "c(3, 3, 3, 6, 6, 6)"       "c(3, 3, 3, 3, 3, 3)"      
[3] "c(29, 29, 29, 30, 30, 30)"

I don't begin to understand this, but I guess these are indices into the levels of the factors of the columns (of the court of king caractacus) of bob? Not what I need.

Strangely I can go through the columns of bob by hand, and do

bob$phenotype <- as.character(bob$phenotype)

which works fine. And, after some typing, I can get a data.frame whose columns are characters rather than factors. So my question is: how can I do this automatically? How do I convert a data.frame with factor columns into a data.frame with character columns without having to manually go through each column?

Bonus question: why does the manual approach work?

Answer 1

Update: Here's an example of something that doesn't work. I thought it would, but I think that the stringsAsFactors option only works on character strings - it leaves the factors alone.

Try this:

bob2 <- data.frame(bob, stringsAsFactors = FALSE)

Generally speaking, whenever you're having problems with factors that should be characters, there's a stringsAsFactors setting somewhere to help you (including a global setting).

Answer 2

The global option

stringsAsFactors: The default setting for arguments of data.frame and read.table.

may be something you want to set yo FALSE in your startup files (e.g. ~/.Rprofile). See help(options).

Answer 3

Another way is to convert it using apply

bob2 <- apply(bob,2,as.character)

And a better one (the previous is of class 'matrix')

bob2 <- as.data.frame(as.matrix(bob),stringsAsFactors=F)

Answer 4

Just following on Matt and Dirk. If you want to recreate your existing data frame without changing the global option, you can recreate it with an apply statement:

bob <- data.frame(lapply(bob, as.character), stringsAsFactors=FALSE)

Answer 5

Or you can try transform:

newbob <- transform(bob, phenotype = as.character(phenotype))

Just be sure to put every factor you'd like to convert to character.

Or you can do something like this and kill all the pests with one blow:

newbob_char <- as.data.frame(lapply(bob[sapply(bob, is.factor)], as.character), stringsAsFactors = FALSE)
newbob_rest <- bob[!(sapply(bob, is.factor))]
newbob <- cbind(newbob_char, newbob_rest)

It's not good idea to shove the data in code like this, I could do the sapply part separately (actually, it's much easier to do it like that), but you get the point... I haven't checked the code, 'cause I'm not at home, so I hope it works! =)

This approach, however, has a downside... you must reorganize columns afterwards, while with transform you can do whatever you like, but at cost of "pedestrian-style-code-writting"...

So there... =)

Answer 6

To replace only factors:

i <- sapply(bob, is.factor)
bob[i] <- lapply(bob[i], as.character)