[adegenet-forum] R adegenet drop loci option

Gary Longo garycharleslongo at gmail.com
Thu Aug 27 02:08:03 CEST 2020


Apologies if I missed this in the forum somewhere but I'm wondering if an
additional option for dropping non-polymorphic loci in `seppop` would be
useful when creating new geninds? Currently the `drop=TRUE` flag drops
non-polymorphic alleles but the monomorphic loci remain in the genind.
Downstream analyses, such as estimating heterozygosity, can be skewed by
these monomorphic loci.

Using `isPoly` works well for getting a list of loci that remain
polymorphic in the new genind, which can then be used to create a new
genind (i.e. `nancycats[loc = new_polymorphic_loci_list]` ). Is this what
most people do?


Gary Charles Longo
NRC Research Associate
NOAA, National Marine Fisheries Service
2725 Montlake Blvd E
Seattle, WA  98112
(831) 247-3056
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