In fact here you don't compute the MAF but the frequency of the second allele.

To get the real maf you can use existing functions (maf in package HardyWeinberg or in vcfR)

You can also compute it easily:

maf 0.5,1-colMeans(geno)/2,colMeans(geno)/2)

or if you keep your "MAF" ()the one you calculated) and you can do only:

geno_filtered 0.05 | MAF < 0.95 )]

For HWE test you can use HWChisq function of package HardyWeinberg or HWE.test in the package genetics.

The question of keeping or removing loci in disequilibrium depends on you question...

You can either use some R packages such as GEN ABEL, SNPassociation or Genetics to do it.

Some very useful R scripts for this purpose or related ones can be found here

http://www.evachan.org/rscripts.html

Cheers

Duy DN

geno_filtered = NAM::snpQC( geno )