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update king for accomodating both plink1 and 2 FID #534

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merged 3 commits into from
Feb 20, 2023
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hsun3163
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  1. Change king2 such that the discrepancy of FID in Different format of snp for Knight(WashU) genotype data #525 should not longer be an issue.
  2. Add pos info in susif module

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@gaow
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gaow commented Feb 20, 2023

dat = dat[!duplicated(dat),]

I wonder if it is logically correct / elegant to have to clean up duplicates like this ... looks like we should have not introduced duplicates in the first place but let me know if you still believe here we know exactly what will be removed rather than ad hoc data clean up ...

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The remove duplicated is a extension from the original function where sorted and remove any Non-uniq IID. The reason that was performed previously is to to remove the the case where
A X B related
B X C related
So we will have A B B C as related individual to be removed.

This is also indicated in the code body now.

@hsun3163 hsun3163 merged commit 8ce51b1 into cumc:main Feb 20, 2023
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