How can I do syntax highlighting for files included with a custom shortcode?

I had a similar issue with WP-Syntax and solved by applying the_content filter in the Shortcode returned values. It would go like:

function my_shortcode( $atts, $content )
{
    $code="<pre class="lang:r">" . $file . '</pre>';   
    return apply_filters ( 'the_content', $code );
}