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VEuPathDB / microbiomeComputations

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Prefilters #78

Closed d-callan closed 8 months ago

d-callan commented 8 months ago

prefilter features/ taxa/ pathway/ etc in AbundanceData based on predicates. ive defined some potentially handy predicate functions as well, but for now am only using the one that removes features if fewer than 50% of samples have data.

implemented for the correlation method, but could be useful for others as well maybe

d-callan commented 8 months ago

I also think it'd be great to replace the hardcoded numbers in the tests with some logic just in case our test data changes

maybe im being dense.. but i didnt see a good way to do this. how many taxa get removed depends pretty directly on the test data used, and i didnt see a good way to find the number without using the same functions i was testing, which kind of defeats the purpose.

d-callan commented 8 months ago

I've realized belatedly that we could pass the default filters/ filters used in the response for clarity. I can do that separately once I get things working.