Why can't I run --fisher with --assoc on PLINK 1.9?

01 August 2023 1 4K Report

I have been trying to generate .assoc file with the Fisher exact test parameter. But PLINK 1.9 is returning the error shown in the picture. I cannot figure out what is going wrong. Glad if somebody could help.

David Morse

Hello Debashruti,

Could you use the freely available R system (which is pretty well vetted and far better known than PLINK (I found a web site that characterizes v 1.9 of plink as "beta" version)?

Here's how to elicit Fisher's exact test in R: https://www.statology.org/fishers-exact-test-in-r/

Good luck with your work.

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