initializing Pendo without using the Snippet

My app was written in CodeIgniter (php) and uses Okta for Authentication. When a user first logs in their email is sent from Okta to my app in a cookie. My app gets the cookie at the top of the first tab (dashboard). This is the code that gets the user's email identifier:

//only run this first time
        if (($this->session->userdata('userid'))==NULL) {
            if (!isset($_COOKIE['email']))   //no cookie show the exit
                exit(0);
            $this->session->set_userdata('userid', $_COOKIE['email']);
        }

If there is no cookie, the app exits. 

For this reason placing the Snippet in the Header will not work because I don't have the email address yet. Once the email is retrieved, it gets stored in a session variable. I can only initialize after the email has been retrieved. 

The API key will come in a similar fashion, via an environment variable. ie it won't be available until the php code grabs it and sticks it in a session variable. 

Is there any example of initializing in the php code itself?