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What Does Nan Mean In Plink'S Sex Check?
        FID         IID       PEDSEX       SNPSEX       STATUS            F
  aaa100000   aaa100000            2            0      PROBLEM          nan
  bbb100000   bbb100000            2            0      PROBLEM       0.4208

I got the above results by doing sex check as

plink --noweb --bfile mydat --check-sex --out mydat

I wonder what nan means in the output. Seems like it is because inbreeding coefficient F cannot be computed but why is that? Thanks for your help.

plink
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updated by pagel • pagel • written by nnlnn • nnlnn

nan or NaN or NA in computing generally refer to something that is "Not A Number". When running statistical tests, NaN can be returned when the statistics cannot be computed, perhaps due to missing values in the data or inappropriately coded data.

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written by Darren J. Fitzpatrick Darren J. Fitzpatrick

Check the X chromosome genotype calls for that individual. Missing data often hoses things.

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written by David Quigley David Quigley

Thanks for the hint. Yes, those with nan F values had completely missing genotypes on the X chromosome.

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written by nnlnn • nnlnn

1 answer

I don't have any experience with this package in particular, but I believe you are correct: it cannot be computed. nan is usually written as NaN and means "not a number." Most likely this results from a division by zero error. Is the inbreeding coefficient of that first individual not calculable because one of its parents is not in the database?

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written by pagel • pagel

Or anything that created an underflow/overflow issue where a number got rounded to 0 due to it being a very small probability for instance.

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written by DG DG

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