Small tests, pre- and post-processing with R may be run in an interactive sessions on the login nodes. All other R jobs have to be submitted through the batch system. An R job (inputfile.R) in batch mode can be started with the following command:
bsub [LSF options] "R --vanilla --slave < inputfile.R > outputfile"
Here [LSF options] needs to be replaced with LSF parameters for the resource requirements of the job. A documentation about the parameters of bsub can be found on the corresponding wiki page about the batch system. In this case, stdout is redirected into "outputfile".