Missing Rate within arrays

Question

[vgenepi]

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

[Kevin Blighe]

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

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

Answer 1

[vgenepi]

I solved with a foreach loop in R.