#!/usr/bin/perl
use strict;
use warnings;

for (@ARGV) {
    next if /P\./; # ignore the P files
    my ($base, $ext)= split /R/; #assume only one 'R' in the file name
    r_p_process ( $base."R".$ext, $base."P".$ext )
}

sub r_p_process {
    my $r_file=shift;
    my $p_file=shift;
    print "processing the pair $r_file $p_file\n";
    # do your funky stuff
}