How do I train my rescue puppy not to snap?

I recently rescued a 2-3 month old Neopolitan Mastiff female that had been attacked by her dad and is still in recovery. She is the sweetest little cuddle-bug and wants affection all the time. Every once in a while when my fiance touches her neck or maybe even startles her she growls and snaps viciously. I understand she is still in pain from her wound, was not socialized to humans, does not feel safe yet in her new environment, and is traumatized by her father biting her so I am hoping that she is still young enough to be trained out of it. What are specific actions that I can do to nip this in the bud while she is still so young?? I have not laid a finger on her so far because I ume that would make things worse. Please give me specific actions I can do! I have looked all over the internet and they all talk about me being dominant and to be ertive not aggressive and so on but what can I do to get her used to being touched on her neck by other people or playing without getting violent and so on?