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Published 20 hours ago • verified publisher icon privefl

control MAF filtering?

Open annilk opened this issue 9 months ago • 3 comments

Hi, when running a GWAS with big_spLinReg I get a message saying that some number of "variables with low/no variation have been removed". I guess this means that some variants have been filtered based on some MAF threshold? Is it possible to control which threshold is applied?

Anni

annilk avatar May 10 '24 15:05 annilk

You must compute the MAFs (e.g. with snp_MAF()), and then provide those that pass some threshold with ind.col = .

privefl avatar May 11 '24 20:05 privefl

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?

annilk avatar May 13 '24 10:05 annilk

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.

privefl avatar May 13 '24 10:05 privefl