Sometimes even the best of friends can get on your nerves, and dealing with annoying friends can be difficult. If you find that a friend annoys you more than he makes you happy, you need to determine whether you want to remain friends or not. If you do, you'll both need to spend time on the friendship to make it work.
Determine what exactly is annoying about this friend, and decide whether the problem is really with your friend or with you. If you're overly sensitive about something your friend does that isn't necessarily annoying, see if this is something you can just put aside. If not, you need to mention your feelings to your friend.
Bring up your feelings with your friend to let her know that her behavior bothers you. If she's willing, see if the two of you can work together to improve her annoying behavior. Let her know how much you value your friendship with her so it doesn't just come across as criticism.
Help her work on stopping this behavior if he agrees, using whatever method he thinks will work. If he starts again, remind him what a great friendship you have and do whatever you've agreed to help him stop.
Ignore the behavior if it keeps happening, and remind yourself how much you value her friendship. Chances are something in her life it making her have these behaviors, especially if what makes her annoying is that she's too clingy or overbearing. Sometimes, though, it's just her personality.
End the friendship if you feel that you can't get over his annoyances and he won't stop being annoying.