[Solved] Extract and paste together multiple columns of a data frame like object using a vector of column names

Question

We may use either of the following:

do.call(function (...) paste(..., sep = "-"), rld[groups])
do.call(paste, c(rld[groups], sep = "-"))

We can consider a small, reproducible example:

rld <- mtcars[1:5, ]
groups <- names(mtcars)[c(1,3,5,6,8)]
do.call(paste, c(rld[groups], sep = "-"))
#[1] "21-160-3.9-2.62-0"     "21-160-3.9-2.875-0"    "22.8-108-3.85-2.32-1" 
#[4] "21.4-258-3.08-3.215-1" "18.7-360-3.15-3.44-0"

Note, it is your responsibility to ensure all(groups %in% names(rld)) is TRUE, otherwise you get “subscript out of bound” or “undefined column selected” error.

(I am copying your comment as a follow-up)

It seems the methods you propose don’t work directly on my object. However, the package I’m using provides a colData function that makes something more similar to a data.frame:

> class(colData(rld))
[1] "DataFrame"
attr(,"package")
[1] "S4Vectors"

do.call(function (...) paste(..., sep = "-"), colData(rld)[groups]) works, but do.call(paste, c(colData(rld)[groups], sep = "-")) fails with an error message I fail to understand (as too often with R…):

> do.call(paste, c(colData(rld)[groups], sep = "-"))
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘mcols’ for signature ‘"character"’

Accepted Answer