Something like SAS or DAP would be better suited for large data sets, as R tends to load everything on the RAM.
From http://www.gnu.org/software/dap/ : "Because Dap processes files one line at a time, rather than reading entire files into memory, it can be, and has been, used on data sets that have very many lines and/or very many variables."
From http://www.gnu.org/software/dap/ : "Because Dap processes files one line at a time, rather than reading entire files into memory, it can be, and has been, used on data sets that have very many lines and/or very many variables."