I regularly use Statistics::R and it works great. You can put all of your R commands within your Perl script, or if you have a lot of R stuff to run, you can use it to specify variables and then run an entire external R script. The examples on the linked page are clear and helpful. Take a look at them and if you have any more questions, let me know.

EDIT: Here is a snippet from one of my Perl scripts which demonstrates setting variables, running R commands from within Perl, and running R scripts from within Perl. The only thing it is really missing is an example of retrieving a value from an R variable (e.g., $value_returned_from_R = $R->get('some.r.variable') ):

my $R = Statistics::R->new();
$R->set( 'filenames', \@filenames );
$R->set( 'id',        $id );
$R->set( 'par1',      $par1 );
$R->set( 'par2',      $par2 );
$R->run_from_file( "genoplot_by_id.build_df.R" );
$R->run_from_file( "genoplot_by_id.build_plot.R" );
$R->run( qq`setwd("$plot_dir")` );
$R->run(
    qq`ggsave(
      filename = paste("$plot_path", "$plot_format", sep = "."),
      plot     = geno.plot,
      width    = $plot_width,
      height   = $plot_height)`
);
[download]

EDIT #2: A couple more examples... Using an array of R commands or a heredoc with multiple R commands (example taken from Statistics::R):

# Array of R commands:
my $out1 = $R->run(
  q`a <- 2`,
  q`b <- 5`,
  q`c <- a * b`,
  q`print("ok")`
);

# Here-doc with multiple R commands:
my $cmds = <<EOF;
a <- 2
b <- 5
c <- a * b
print('ok')
EOF
my $out2 = $R->run($cmds);
[download]

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