I would just leave it for a while, wait til the awkwardness passes? If it's taking too long to pass, I would text her saying "Sorry if you're annoyed, I was just uncomfortable. Friends?" and if she does it again then I really do think you should talk to her - even just ask her to do it when you aren't in. Could you not make a joke out of it? I find that makes me less awkward, to just have a go in a light-hearted fashion that still lets them know it bothers you without it being too awkward.
It'll be fine if she's your best friend :)
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