Weighted ORA #66
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Weighted ORA #66
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cthoyt
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This PR contains a first attempt at implementing a weighted variant of ORA based on evidence counts. I'll try and write up a mathematical description later, but the main difference between normal ORA and weighted ORA is that in normal ORA, the weights for each gene in the pathway are either 1.0 or 0.0, and you can assume the ones that aren't explicitly given are 0.0. In weighted ORA, you're only given the positive ones and can't really assume anything about the others, so my solution was to assign all of them the average of the given values with a scaling factor such that if the weights are actually just given as 1.0 each, this becomes the special case of normal ORA.