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Missing Rate within arrays

Hi everyone! I need to estimate Missing rates for each SNP within each array. I have a file with FID and Array ID. My cluster variable is the array ID. This command should help me: ./plink --bfile mydata --loop-assoc array.lst --missing The file array.lst is with three columns: FID, column of 1s, and ArrayID. Each person is in one array only. But Plink does not recognize the clusters. Is there someone could help me? Thanks a lot

snp call rate array plink
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written by vgenepi • vgenepi

Why do you need the file array.lst if you just want the missingness per sample?

This should work: plink --bfile mydata --missing

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written by Kevin Blighe Kevin Blighe

1 answer

I solved with a foreach loop in R.

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written by vgenepi • vgenepi

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