You want to make sure to let HER make the first move. If you try to "make" her affectionate, and she's not ready, you will make it much worse. Let her come to you. You are much bigger than her, and you *can* pick her up whenever you want. That can be threatening to a cat if they don't trust you. She needs to be able to hide when she wants, and when she hides, you cannot bring her out of her hiding spot, or she won't feel safe around you. Give her some space -- sit a few feet away from her, try not to pick her up, and don't force any contact with her. This way, she'll know that you are not a threat, and you are not aggressive, and hopefully she'll start to relax, and come to YOU, or at least tolerate it when you move closer to her for petting. It might take some time, but it has to happen if you want her to calm down.
Is she spayed? If she's not, she should be. This could have a MAJOR affect on her personality.