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myles-lewis / glmmSeq

Gene-level general linear mixed model
https://myles-lewis.github.io/glmmSeq/
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Specify design matrix #17

Closed zktuong closed 2 years ago

zktuong commented 2 years ago

Hi, thanks for this really great package!

I'm wanting to run a model that contains an ordered categorical factor (condition A > condition B > condition C) and made some adjustments to the code to allow a designMatrix option to basically overwrite the designMatrix to respect the way it would have been constructed if ordered factors were in the metadata; the columns would contain the levels of the ordered factor from 2 to 4 (.L, .Q, .C, ^4 instead of A,B,C). This is probably not the cleanest way to proceed but i think it sort of works. I'm not exactly sure how to compute the LFC from this but i can make do with the estimates for now.

Best regards, Kelvin

KatrionaGoldmann commented 2 years ago

Great thanks. This is a good idea, I have merged in your changes.