Actually, I get the exact same output from both solutions, which works just great for me :) So thank you both.

I end up with:

$VAR1 = {
          'R1' => {
                  },
          'R2' => {
                  }
             ...
        };
$VAR1 = {
          'R1' => {
                  },
          'R2' => {
                  }
             ...
        };
         ...
[download]

However, I will be using:

foreach my $lig (keys %{$ligHash})
{
    findIntersection($ligHash->{$lig}, $lig);
}
[download]

Because it gives me the option to easily pass the hash name (i.e. '34k') as a string.

Did either of you intend on a different output? If so I would be interested in that as well.