How do I clear this setInterval inside a function?

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The setInterval method returns a handle that you can use to clear the interval. If you want the function to return it, you just return the result of the method call:

function intervalTrigger() {
  return window.setInterval( function() {
    if (timedCount >= markers.length) {
       timedCount = 0;
    }
    google.maps.event.trigger(markers[timedCount], "click");
    timedCount++;
  }, 5000 );
};
var id = intervalTrigger();

Then to clear the interval:

window.clearInterval(id);

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