Short and sweet, add the following two lines where you want to trigger a javascript function. Just change the javascript denoted in the code by "javascriptFunction()" with whatever you want to call. Also jsut in case make sure you have the allowScriptAccess parameter set to "always".

var runJavascript:URLRequest = new URLRequest("javascript:javascriptFunction()");
navigateToURL(runJavascript, "_top");