Comments (3)
privefl
commented on June 15, 2024
You must compute the MAFs (e.g. with snp_MAF()), and then provide those that pass some threshold with ind.col = .
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annilk
commented on June 15, 2024
Ok, thanks! I will use that.
How the variables are filtered when user does not provide any indices for ind.col? Is there some default threshold for MAF?
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privefl
commented on June 15, 2024
There is no MAF threshold since this function is not specific to genetic data; it can be used for any matrices.
IIRC, the function checks for standard deviations lower than 1e-6 and remove those.
This would correspond to a very small MAF threshold. Basically it checks that it is different from 0.
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