Seamus was very, very timid when I first got him, and hissed whenever I found him in his hiding spot. The only reason I would even bother to look for him was because I never, ever saw him out for at least a couple weeks and I wanted to assure he was ok.
He had a few good hiding spots under the bed, in the closet, and a few I still don't know how he managed (under a dresser!) When he was in hiding, I would completely ignore him... within weeks he was curious about where he was living, and I would give him his space when he explored. Then he would sit on a dining room chair under the table, which gave him the view he wanted of everything around him but kept me away. A few times I attempted to get close, and he hissed, so I just let him be... within a few weeks, he got a little more comfortable and would sit on a pillow near the couch when I was on the couch. I would play with him with a dangling toy and give him treats, but again, never too close... he was my first cat too, so it was all trial and error, and if I do adopt another cat, I'm somewhat inclined to take in another special case like his because I learned I have the patience for it. Eventually, he got the hint that I was nurturing and not harmful and now, you'd never know he was who he was two years ago... he looks for cuddles and gets mad when I'm not right there.
My best advice, just be patient, stay out of her way when she's in a mood. The upside, she comes for petting and kind of knows you're ok... (took my boy 6 months to even let me pet him) She's still figuring out whether or not you're ok, her trust isn't 100% yet. It seems her hiss is the warning "Don't come near me right now!" Talk softly and soothe her from a distance when she gets like that... I talked to Seamus a lot in the beginning, and when I talked, he responded to my voice by coming closer each time. She just needs reassurance that you're ok all the time, not just when she wants to be pet... don't get discouraged, she'll get there.